28:null 29:["$","title",null,{"children":"Nanopore Sequencing Scripts for Mac | WabushOnce | Observable"}] 2e:T4b2,# Nanopore Sequencing Scripts for Mac - [**Dorado Version Check**](#DoradoVersion): Ensure the latest Dorado Base-caller is Used - [**Dorado Basecalling**](#Dorado): Convert Nanopore voltage signals (.pod5) to reads (.fastq) - [**Demultiplexing**](#Demultiplexing): Split barcoded reads into individual barcode folders - [**Merge Barcodes**](#Merge_Barcodes): Combine multiple barcode .fasta files into one .fasta file - [**Remove Host Reads**](#Remove_Host): Remove Host Reads from .fastQ files - [**NanoComp or NanoPlot**](#NanoPlot): Assess the quality of the sequence reads - [**Filter Reads**](#Filter_Filtlong): Filter reads using FiltLong or Chopper - [**Flye**](#Flye): Use Flye to assemble by barcode and polish using Racon & Medaka - [**View Read Coverage**](#Create_BAM): Create .bam and .sam files to view read coverage - [**Pharokka**](#PharokkaAnnotation): Annotate phage FastA genomes - [**Batch Rename**](#BatchRename): Batch Rename Folders and Files ## Analysis BlastN Fasta Contigs: - Blast Contigs tool opens a FastA, displays all contigs contigs, and quickly BlastN each contig on PhagesDB or NCBI. --- 2f:Ta14,viewof doradoChecker = { const releasesUrl = "https://github.com/nanoporetech/dorado/releases/latest"; const buttonStyle = ` padding: 0.5em 0.85em; border: 1px solid #bbb; border-radius: 6px; background: #f7f7f7; cursor: pointer; font-size: 0.9em; `; const latest = html`Not checked`; const checkBtn = html``; const openBtn = html``; const copyBtn = html``; const cmd = `conda activate reads-assembly-core && command -v dorado && dorado --version`; const codeBox = html`

${cmd}

`; function parseVersion(str) { const m = (str || "").match(/[0-9]+(?:\.[0-9]+)*/); return m ? m[0] : "unknown"; } checkBtn.onclick = async () => { latest.textContent = "checking..."; try { const resp = await fetch( "https://api.github.com/repos/nanoporetech/dorado/releases/latest" ); const data = await resp.json(); latest.textContent = parseVersion(data.tag_name); } catch (err) { latest.textContent = "check failed"; } }; openBtn.onclick = () => { window.open(releasesUrl, "_blank", "noopener,noreferrer"); }; copyBtn.onclick = () => { navigator.clipboard.writeText(cmd); copyBtn.textContent = "✅ Copied"; setTimeout(() => { copyBtn.textContent = "📋 Copy Mac Script code"; }, 1200); }; return html`

Dorado version checker

Use the latest basecaller for improved accuracy.
Latest Dorado version: ${latest}

${checkBtn} ${openBtn}

To check your installed version, copy and run the code below in WSL:

${copyBtn} ${codeBox}

`; }30:T479d,viewof doradoMacInstaller = { ///////////////////////////////////////////////////////////////////////////// // INPUT ///////////////////////////////////////////////////////////////////////////// const envInput = Inputs.text({ label: "Conda environment name", value: "reads-assembly-core", placeholder: "reads-assembly-core", style: "width:340px; max-width:100%;" }); ///////////////////////////////////////////////////////////////////////////// // SHARED STYLES ///////////////////////////////////////////////////////////////////////////// const buttonStyle = ` padding:0.5em 0.85em; border:1px solid #bbb; border-radius:6px; background:#f7f7f7; cursor:pointer; font-size:0.9em; `; ///////////////////////////////////////////////////////////////////////////// // BUTTONS AND OUTPUT ELEMENTS ///////////////////////////////////////////////////////////////////////////// const copyButton = html` `; const downloadButton = html` `; const status = html`

`; const textarea = html` `; const arrow = html` ▶ `; ///////////////////////////////////////////////////////////////////////////// // COLLAPSIBLE PANEL ///////////////////////////////////////////////////////////////////////////// const panel = html`

${arrow} Dorado installer generator - macOS 15

Creates the selected Conda environment when needed, installs the latest Dorado release for Apple Silicon, and verifies the installed version.

${envInput}

${copyButton} ${downloadButton}

${status}

Copy the complete generated code and paste it into the macOS Terminal.

${textarea}

`; /* * Hide Observable/browser's default disclosure arrow because the panel * uses the custom ▶ and ▼ arrow above. */ const root = html`

${panel}

`; ///////////////////////////////////////////////////////////////////////////// // INSTALLER GENERATOR ///////////////////////////////////////////////////////////////////////////// function buildInstaller(envName) { /* * Bash expressions beginning with ${ * are temporarily represented by __BASH_OPEN__. * * This prevents Observable JavaScript from interpreting Bash parameter * expansion expressions. */ const template = String.raw`bash <<'DORADO_INSTALLER' #!/usr/bin/env bash set -Eeo pipefail WORKDIR="" cleanup() { if [ -n "$WORKDIR" ] && [ -d "$WORKDIR" ]; then rm -rf "$WORKDIR" fi } trap cleanup EXIT trap 'status=$?; echo; echo "❌ Dorado installation failed at line $LINENO (exit $status)"; exit $status' ERR export PATH="/opt/homebrew/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:__BASH_OPEN__PATH:-}" CONDA_ENV='__CONDA_ENV__' printf '\n🧬 Dorado installer for macOS\n' printf '=============================\n\n' ############################################################################### # CHECK MACOS AND PROCESSOR ARCHITECTURE ############################################################################### if [ "$(uname -s)" != "Darwin" ]; then echo "❌ This installer must be run on macOS." exit 1 fi ARCH=$(uname -m) if [ "$ARCH" != "arm64" ]; then echo "❌ Dorado for macOS requires an Apple Silicon Mac." echo echo "Detected architecture:" echo " $ARCH" exit 1 fi MACOS_VERSION=$(sw_vers -productVersion) MACOS_MAJOR=__BASH_OPEN__MACOS_VERSION%%.*} case "$MACOS_MAJOR" in ''|*[!0-9]*) echo "❌ Could not determine the macOS version." exit 1 ;; esac if [ "$MACOS_MAJOR" -lt 14 ]; then echo "❌ Dorado requires macOS 14 or newer." echo echo "Detected macOS:" echo " $MACOS_VERSION" exit 1 fi echo "✅ macOS: $MACOS_VERSION" echo "✅ Architecture: $ARCH" echo "🧪 Conda environment: $CONDA_ENV" ############################################################################### # CHECK REQUIRED COMMANDS ############################################################################### echo echo "🔎 Checking required commands..." for REQUIRED_COMMAND in \ awk \ curl \ grep \ head \ mktemp \ sw_vers \ uname \ unzip do if ! command -v "$REQUIRED_COMMAND" >/dev/null 2>&1; then echo "❌ Required command not found:" echo " $REQUIRED_COMMAND" exit 1 fi done echo "✅ Required commands are available." ############################################################################### # LOCATE CONDA ############################################################################### echo echo "🔎 Locating Conda..." CONDA_SH="" if command -v conda >/dev/null 2>&1; then CONDA_BASE=$( conda info --base 2>/dev/null || true ) if [ -n "$CONDA_BASE" ] && [ -f "$CONDA_BASE/etc/profile.d/conda.sh" ]; then CONDA_SH="$CONDA_BASE/etc/profile.d/conda.sh" fi fi if [ -z "$CONDA_SH" ]; then for CONDA_BASE in \ /opt/miniconda3 \ /opt/miniforge3 \ /opt/anaconda3 \ "$HOME/miniconda3" \ "$HOME/miniforge3" \ "$HOME/anaconda3" \ "$HOME/mambaforge" \ "$HOME/miniconda" do if [ -f "$CONDA_BASE/etc/profile.d/conda.sh" ]; then CONDA_SH="$CONDA_BASE/etc/profile.d/conda.sh" break fi done fi if [ -z "$CONDA_SH" ]; then echo "❌ Conda was not found." echo echo "Install Miniconda or Miniforge, then run this installer again." exit 1 fi /* * Conda activation and deactivation hooks can reference optional variables. * Leave nounset disabled until the requested environment is active. */ set +u . "$CONDA_SH" if ! command -v conda >/dev/null 2>&1; then echo "❌ Conda was unavailable after loading:" echo " $CONDA_SH" exit 1 fi echo "✅ Conda base:" echo " $(conda info --base)" ############################################################################### # CREATE THE CONDA ENVIRONMENT WHEN MISSING ############################################################################### echo echo "🔎 Checking Conda environment:" echo " $CONDA_ENV" ENV_EXISTS=0 while IFS= read -r ENV_PATH do [ -n "$ENV_PATH" ] || continue if [ "$(basename "$ENV_PATH")" = "$CONDA_ENV" ]; then ENV_EXISTS=1 break fi done < <( conda env list | awk ' /^[[:space:]]*#/ { next } NF == 0 { next } { print $NF } ' ) if [ "$ENV_EXISTS" -eq 1 ]; then echo "✅ Environment already exists:" echo " $CONDA_ENV" else echo "📦 Creating environment:" echo " $CONDA_ENV" if ! conda create \ -y \ -n "$CONDA_ENV" \ python=3.11 \ pip then echo echo "❌ Conda could not create the environment:" echo " $CONDA_ENV" exit 1 fi echo "✅ Environment created successfully." fi ############################################################################### # ACTIVATE THE CONDA ENVIRONMENT ############################################################################### echo echo "🔄 Activating environment..." if ! conda activate "$CONDA_ENV"; then echo echo "❌ Could not activate Conda environment:" echo " $CONDA_ENV" echo echo "Available environments:" conda env list || true exit 1 fi if [ -z "__BASH_OPEN__CONDA_PREFIX:-}" ]; then echo "❌ CONDA_PREFIX is empty after activation." exit 1 fi /* * Restore nounset after Conda has finished switching environments. */ set -u echo "✅ Active environment:" echo " $CONDA_PREFIX" ############################################################################### # CHECK THE CURRENTLY INSTALLED DORADO VERSION ############################################################################### CURRENT_DIR="$CONDA_PREFIX/dorado-current" CURRENT_BINARY="$CURRENT_DIR/bin/dorado" WRAPPER="$CONDA_PREFIX/bin/dorado" INSTALLED_VERSION="none" if [ -x "$CURRENT_BINARY" ]; then INSTALLED_VERSION=$( "$CURRENT_BINARY" --version 2>&1 | grep -Eo '[0-9]+([.][0-9]+){2}' | head -n1 || true ) INSTALLED_VERSION=__BASH_OPEN__INSTALLED_VERSION:-none} fi echo echo "🔎 Installed Dorado version:" echo " $INSTALLED_VERSION" ############################################################################### # DETERMINE THE LATEST DORADO RELEASE ############################################################################### echo echo "🌐 Checking the latest Dorado release..." LATEST_URL=$( curl \ -fLsS \ --retry 3 \ --retry-delay 2 \ --connect-timeout 30 \ -o /dev/null \ -w '%{url_effective}' \ https://github.com/nanoporetech/dorado/releases/latest ) LATEST_URL=__BASH_OPEN__LATEST_URL%/} LATEST_TAG=__BASH_OPEN__LATEST_URL##*/} LATEST_VERSION=__BASH_OPEN__LATEST_TAG#v} if ! printf '%s\n' "$LATEST_VERSION" | grep -Eq '^[0-9]+[.][0-9]+[.][0-9]+$' then echo "❌ Could not determine the latest Dorado version." echo echo "GitHub returned:" echo " $LATEST_URL" exit 1 fi echo "🌐 Latest Dorado version:" echo " $LATEST_VERSION" ############################################################################### # DOWNLOAD AND INSTALL DORADO ############################################################################### if [ "$INSTALLED_VERSION" != "$LATEST_VERSION" ] || [ ! -x "$CURRENT_BINARY" ]; then WORKDIR=$( mktemp -d "__BASH_OPEN__TMPDIR:-/tmp}/dorado-install.XXXXXX" ) if [ -z "$WORKDIR" ] || [ ! -d "$WORKDIR" ]; then echo "❌ Could not create a temporary installation directory." exit 1 fi cd "$WORKDIR" ARCHIVE="dorado-__BASH_OPEN__LATEST_VERSION}-osx-arm64.zip" EXTRACTED_NAME="dorado-__BASH_OPEN__LATEST_VERSION}-osx-arm64" DOWNLOAD_URL="https://cdn.oxfordnanoportal.com/software/analysis/$ARCHIVE" echo echo "⬇️ Downloading Dorado:" echo " $DOWNLOAD_URL" curl \ -fL \ --retry 3 \ --retry-delay 2 \ --connect-timeout 30 \ -o "$ARCHIVE" \ "$DOWNLOAD_URL" if [ ! -s "$ARCHIVE" ]; then echo "❌ The downloaded archive is empty." exit 1 fi echo echo "🔍 Checking archive..." unzip -tq "$ARCHIVE" >/dev/null echo "✅ Archive passed the integrity check." echo echo "📦 Extracting Dorado..." unzip -q "$ARCHIVE" EXTRACTED_DIR="$WORKDIR/$EXTRACTED_NAME" if [ ! -x "$EXTRACTED_DIR/bin/dorado" ]; then echo "❌ Dorado executable was not found after extraction." echo echo "Expected:" echo " $EXTRACTED_DIR/bin/dorado" exit 1 fi NEW_DIR="$CONDA_PREFIX/$EXTRACTED_NAME" echo echo "📂 Installing Dorado into:" echo " $NEW_DIR" rm -rf "$NEW_DIR" mv "$EXTRACTED_DIR" "$NEW_DIR" rm -rf "$CURRENT_DIR" ln -s "$NEW_DIR" "$CURRENT_DIR" xattr \ -dr \ com.apple.quarantine \ "$NEW_DIR" \ 2>/dev/null || true CURRENT_BINARY="$CURRENT_DIR/bin/dorado" echo "✅ Dorado files installed." else echo echo "✅ Dorado is already up to date." fi ############################################################################### # CHECK THE INSTALLED EXECUTABLE ############################################################################### if [ ! -x "$CURRENT_BINARY" ]; then echo "❌ Dorado is not executable after installation." exit 1 fi ############################################################################### # CREATE THE DORADO COMMAND ############################################################################### mkdir -p "$CONDA_PREFIX/bin" cat > "$WRAPPER" </dev/null 2>&1; then echo "❌ Dorado was installed, but the executable check failed." exit 1 fi ############################################################################### # INSTALLATION SUMMARY ############################################################################### echo echo "✅ Dorado installation completed successfully." echo echo "Dorado installation:" echo " $CURRENT_DIR" echo echo "Conda environment:" echo " $CONDA_ENV" echo echo "To use Dorado later:" echo echo " conda activate $CONDA_ENV" echo " dorado --version" echo DORADO_INSTALLER`; return template .split("__BASH_OPEN__") .join("${") .split("__CONDA_ENV__") .join(envName); } ///////////////////////////////////////////////////////////////////////////// // UPDATE DISPLAY ///////////////////////////////////////////////////////////////////////////// function update() { const envName = String(envInput.value ?? "").trim(); const isValid = /^[A-Za-z0-9._-]+$/.test(envName); if (!isValid) { textarea.value = ""; copyButton.disabled = true; downloadButton.disabled = true; copyButton.style.cursor = "not-allowed"; downloadButton.style.cursor = "not-allowed"; copyButton.style.opacity = "0.55"; downloadButton.style.opacity = "0.55"; status.textContent = "❌ Use only letters, numbers, periods, underscores, or hyphens."; status.style.color = "#b42318"; } else { textarea.value = buildInstaller(envName); copyButton.disabled = false; downloadButton.disabled = false; copyButton.style.cursor = "pointer"; downloadButton.style.cursor = "pointer"; copyButton.style.opacity = "1"; downloadButton.style.opacity = "1"; status.textContent = `✅ Installer ready. It will install Dorado in "${envName}".`; status.style.color = "#067647"; } root.value = { condaEnvironment: envName, code: textarea.value }; root.dispatchEvent( new Event("input", { bubbles: true }) ); } ///////////////////////////////////////////////////////////////////////////// // PANEL ARROW ///////////////////////////////////////////////////////////////////////////// panel.addEventListener("toggle", () => { arrow.textContent = panel.open ? "▼" : "▶"; }); ///////////////////////////////////////////////////////////////////////////// // INPUT LISTENER ///////////////////////////////////////////////////////////////////////////// envInput.addEventListener("input", update); ///////////////////////////////////////////////////////////////////////////// // COPY BUTTON ///////////////////////////////////////////////////////////////////////////// copyButton.addEventListener("click", async () => { if (copyButton.disabled) { return; } try { await navigator.clipboard.writeText(textarea.value); } catch (error) { textarea.focus(); textarea.select(); document.execCommand("copy"); } copyButton.textContent = "✅ Copied"; status.textContent = "✅ Installer copied to the clipboard."; status.style.color = "#067647"; setTimeout(() => { copyButton.textContent = "📋 Copy installer"; }, 1200); }); ///////////////////////////////////////////////////////////////////////////// // DOWNLOAD BUTTON ///////////////////////////////////////////////////////////////////////////// downloadButton.addEventListener("click", () => { if (downloadButton.disabled) { return; } const blob = new Blob([textarea.value], { type: "text/x-shellscript;charset=utf-8" }); const url = URL.createObjectURL(blob); const link = document.createElement("a"); link.href = url; link.download = "install_dorado_macos15.sh"; document.body.appendChild(link); link.click(); link.remove(); URL.revokeObjectURL(url); downloadButton.textContent = "✅ Downloaded"; status.textContent = "✅ install_dorado_macos15.sh was created."; status.style.color = "#067647"; setTimeout(() => { downloadButton.textContent = "⬇️ Download .sh"; }, 1200); }); update(); return root; }31:T56d8,viewof doradoMacBasecallDemuxGenerator = { ///////////////////////////////////////////////////////////////////////////// // INPUT CONTROLS ///////////////////////////////////////////////////////////////////////////// const makeText = (label, value, placeholder = "") => Inputs.text({ label, value, placeholder, style: "width:100%;" }); const condaEnvironment = makeText( "🧪 Conda environment", "reads-assembly-core", "reads-assembly-core" ); const doradoExecutable = makeText( "🧬 Dorado command or executable path", "dorado", "/opt/miniconda3/envs/reads-assembly-core/bin/dorado" ); const pod5Directory = makeText( "📂 POD5 input folder", "/Users/name/Desktop/Nanopore_Results/Run2/pod5", "/Users/name/Desktop/.../pod5" ); const outputDirectory = makeText( "📁 Output folder", "/Users/name/Desktop/Nanopore_Results/Run2", "/Users/name/Desktop/.../Run2" ); const barcodeArrangement = makeText( "🏷️ Custom barcode arrangement TOML", "/Users/name/Desktop/Nanopore_Results/CustomBarcode_Files/M13-pl27f.toml", "/Users/name/Desktop/.../M13-pl27f.toml" ); const barcodeSequences = makeText( "🧬 Custom barcode sequences FASTA", "/Users/name/Desktop/Nanopore_Results/CustomBarcode_Files/pl27f.fasta", "/Users/name/Desktop/.../pl27f.fasta" ); const model = makeText( "🧠 Dorado model", "dna_r10.4.1_e8.2_400bps_sup@v5.2.0" ); const kitName = makeText("🏷️ Custom barcode kit name", "PL27f"); const bamFilename = makeText( "📄 Basecalled BAM filename", "Dorado_Output.bam" ); const demuxFolderName = makeText( "📂 Demultiplexed FASTQ folder name", "Demux_Output" ); const scriptFilename = makeText( "💾 Downloaded script filename", "dorado_basecall_demux_mac.command" ); const minQscore = Inputs.number({ label: "📊 Minimum Q-score", value: 10, min: 0, step: 1 }); const device = Inputs.select(["auto", "cpu"], { label: "⚙️ Compute device", value: "auto" }); const options = Inputs.checkbox( [ "Search POD5 subfolders recursively", "Show verbose Dorado output", "Require matching barcodes at both ends", "Pause before the Terminal window closes" ], { label: "Additional options", value: [ "Search POD5 subfolders recursively", "Show verbose Dorado output", "Pause before the Terminal window closes" ] } ); ///////////////////////////////////////////////////////////////////////////// // OUTPUT ELEMENTS ///////////////////////////////////////////////////////////////////////////// const textarea = html``; const validation = html`

`; const copyButton = html``; const downloadButton = html``; ///////////////////////////////////////////////////////////////////////////// // LAYOUT ///////////////////////////////////////////////////////////////////////////// const controls = html`

`; [ condaEnvironment, doradoExecutable, pod5Directory, outputDirectory, barcodeArrangement, barcodeSequences, model, kitName, minQscore, device, bamFilename, demuxFolderName, scriptFilename, options ].forEach((control) => controls.append(control)); const instructions = html`

The copied code is wrapped in a Bash heredoc so it can be pasted safely into macOS Terminal without the zsh event not found: /usr/bin/env error.

Enter complete Mac paths beginning with /Users/ or /Volumes/.

`; const buttonRow = html`

`; buttonRow.append(copyButton, downloadButton); controls.prepend(instructions); controls.append(buttonRow, validation); const codePanel = html`

Generated macOS Terminal code

`; codePanel.append(textarea); const expandedContent = html`

`; expandedContent.append(controls, codePanel); const details = html`

🧬 Generate Dorado basecalling and demultiplexing code for macOS

`; details.append(expandedContent); ///////////////////////////////////////////////////////////////////////////// // HELPER FUNCTIONS ///////////////////////////////////////////////////////////////////////////// function shellQuote(value) { return `'${String(value ?? "").replace(/'/g, `'\\''`)}'`; } function selected(label) { return Array.isArray(options.value) && options.value.includes(label); } function safeDownloadName(value) { let name = String(value || "dorado_basecall_demux_mac.command") .trim() .replace(/[\\/:*?"<>|]/g, "_"); if (!name.toLowerCase().endsWith(".command")) { name += ".command"; } return name || "dorado_basecall_demux_mac.command"; } ///////////////////////////////////////////////////////////////////////////// // VALIDATION ///////////////////////////////////////////////////////////////////////////// function getIssues() { const issues = []; const envValue = String(condaEnvironment.value || "").trim(); if (!envValue) { issues.push("The Conda environment name is empty."); } else if (!/^[A-Za-z0-9._-]+$/.test(envValue)) { issues.push( "The Conda environment name may contain only letters, numbers, periods, underscores, and hyphens." ); } const pathFields = [ ["POD5 folder", pod5Directory.value], ["Output folder", outputDirectory.value], ["Barcode TOML", barcodeArrangement.value], ["Barcode FASTA", barcodeSequences.value] ]; for (const [label, rawValue] of pathFields) { const value = String(rawValue || "").trim(); if (!value) { issues.push(`${label} is empty.`); } else if (/^[A-Za-z]:[\\/]/.test(value)) { issues.push( `${label} is a Windows path. Enter a Mac path beginning with /Users/ or /Volumes/.` ); } else if (/^\/mnt\/[a-z]\//i.test(value)) { issues.push( `${label} is a WSL path. Enter the corresponding Mac path.` ); } else if (!value.startsWith("/")) { issues.push(`${label} should be a complete Mac path beginning with /.`); } } const doradoValue = String(doradoExecutable.value || "").trim(); if (!doradoValue) { issues.push("The Dorado command or executable path is empty."); } else if ( /^[A-Za-z]:[\\/]/.test(doradoValue) || /^\/mnt\//i.test(doradoValue) ) { issues.push("The Dorado executable uses a Windows or WSL path."); } else if (doradoValue.includes("/") && !doradoValue.startsWith("/")) { issues.push( 'Use either "dorado" or a complete absolute path to the Dorado executable.' ); } if (!String(model.value || "").trim()) { issues.push("The Dorado model is empty."); } if (!String(kitName.value || "").trim()) { issues.push("The custom barcode kit name is empty."); } if (!String(bamFilename.value || "").trim()) { issues.push("The BAM filename is empty."); } if (!String(demuxFolderName.value || "").trim()) { issues.push("The demultiplexed FASTQ folder name is empty."); } return issues; } ///////////////////////////////////////////////////////////////////////////// // SCRIPT GENERATOR ///////////////////////////////////////////////////////////////////////////// function buildRawCommandScript() { const recursiveFlag = selected("Search POD5 subfolders recursively"); const verboseFlag = selected("Show verbose Dorado output"); const bothEndsFlag = selected("Require matching barcodes at both ends"); const pauseAtEnd = selected("Pause before the Terminal window closes"); const basecallerArguments = [ '"$MODEL"', '"$POD5_DIR"', '--device "$DEVICE"', '--min-qscore "$MIN_QSCORE"', '--kit-name "$KIT_NAME"', '--barcode-arrangement "$BARCODE_ARRANGEMENT"', '--barcode-sequences "$BARCODE_SEQUENCES"' ]; if (recursiveFlag) { basecallerArguments.splice(2, 0, "--recursive"); } if (verboseFlag) { basecallerArguments.splice(2, 0, "--verbose"); } if (bothEndsFlag) { basecallerArguments.push("--barcode-both-ends"); } const formattedBasecallerArguments = basecallerArguments .map((argument) => ` ${argument}`) .join(" \\\n"); const basecallerCommand = `"$DORADO" basecaller \\\n` + `${formattedBasecallerArguments} \\\n` + ` > "$OUT_BAM"`; const demuxCommand = [ '"$DORADO" demux', ' --output-dir "$DEMUX_DIR"', " --no-classify", " --emit-fastq", ' "$OUT_BAM"' ].join(" \\\n"); const commandFilename = safeDownloadName(scriptFilename.value); return `#!/usr/bin/env bash # 🧬 Dorado basecall + demux for macOS Apple Silicon # Generated by an Observable notebook. # # Run a downloaded file from Terminal with: # # chmod +x "${commandFilename}" # "./${commandFilename}" set -Eeuo pipefail pause_if_interactive() { if [[ -t 0 ]]; then echo read -r -p "Press Enter to close..." _ fi } on_error() { status=$? line=$1 echo echo "❌ Script failed at line $line (exit $status)" pause_if_interactive exit "$status" } trap 'on_error "$LINENO"' ERR ############################################################################### # USER SETTINGS ############################################################################### CONDA_ENV=${shellQuote(String(condaEnvironment.value || "").trim())} DORADO=${shellQuote(String(doradoExecutable.value || "").trim())} POD5_DIR=${shellQuote(String(pod5Directory.value || "").trim())} OUTPUT_DIR=${shellQuote(String(outputDirectory.value || "").trim())} BARCODE_ARRANGEMENT=${shellQuote(String(barcodeArrangement.value || "").trim())} BARCODE_SEQUENCES=${shellQuote(String(barcodeSequences.value || "").trim())} MODEL=${shellQuote(String(model.value || "").trim())} KIT_NAME=${shellQuote(String(kitName.value || "").trim())} MIN_QSCORE=${shellQuote( Number.isFinite(Number(minQscore.value)) ? Number(minQscore.value) : 10 )} DEVICE=${shellQuote(String(device.value || "auto"))} BAM_FILENAME=${shellQuote( String(bamFilename.value || "Dorado_Output.bam").trim() )} DEMUX_FOLDER_NAME=${shellQuote( String(demuxFolderName.value || "Demux_Output").trim() )} OUT_BAM="$OUTPUT_DIR/$BAM_FILENAME" DEMUX_DIR="$OUTPUT_DIR/$DEMUX_FOLDER_NAME" ############################################################################### # SYSTEM CHECKS ############################################################################### if [[ "$(uname -s)" != "Darwin" ]]; then echo "❌ This script is intended for macOS." pause_if_interactive exit 1 fi if [[ "$(uname -m)" != "arm64" ]]; then echo "❌ The supported Dorado macOS build requires an Apple-silicon Mac." echo "Detected architecture: $(uname -m)" pause_if_interactive exit 1 fi ############################################################################### # LOAD CONDA AND ACTIVATE THE DORADO ENVIRONMENT ############################################################################### CONDA_SH="" if command -v conda >/dev/null 2>&1; then CONDA_BASE=$(conda info --base 2>/dev/null || true) if [[ -n "$CONDA_BASE" ]] && [[ -f "$CONDA_BASE/etc/profile.d/conda.sh" ]]; then CONDA_SH="$CONDA_BASE/etc/profile.d/conda.sh" fi fi if [[ -z "$CONDA_SH" ]]; then for CONDA_BASE in \ /opt/miniconda3 \ /opt/miniforge3 \ /opt/anaconda3 \ "$HOME/miniconda3" \ "$HOME/miniforge3" \ "$HOME/anaconda3" \ "$HOME/mambaforge" \ "$HOME/miniconda" do if [[ -f "$CONDA_BASE/etc/profile.d/conda.sh" ]]; then CONDA_SH="$CONDA_BASE/etc/profile.d/conda.sh" break fi done fi if [[ -z "$CONDA_SH" ]]; then echo "❌ Conda could not be found." pause_if_interactive exit 1 fi # Conda activation may run deactivate.d/activate.d hook scripts that read # optional backup variables. Temporarily disable Bash nounset so those Conda # scripts do not fail when an optional variable has not been defined. set +u . "$CONDA_SH" if ! conda activate "$CONDA_ENV"; then echo "❌ Could not activate Conda environment: $CONDA_ENV" echo conda env list || true pause_if_interactive exit 1 fi # Restore strict checking after Conda has finished changing environments. set -u if [[ -z "\${CONDA_PREFIX:-}" ]]; then echo "❌ CONDA_PREFIX is empty after activating $CONDA_ENV." pause_if_interactive exit 1 fi echo "✅ Active Conda environment: $CONDA_ENV" echo " $CONDA_PREFIX" ############################################################################### # DORADO CHECK ############################################################################### if [[ "$DORADO" == */* ]]; then if [[ ! -x "$DORADO" ]]; then echo "❌ Dorado executable not found or not executable:" echo "$DORADO" pause_if_interactive exit 1 fi else if ! command -v "$DORADO" >/dev/null 2>&1; then echo "❌ Dorado was not found after activating $CONDA_ENV." echo echo "Expected the command to be available as: $DORADO" echo "Check with: conda activate $CONDA_ENV && dorado --version" pause_if_interactive exit 1 fi DORADO=$(command -v "$DORADO") fi ############################################################################### # INPUT FILE CHECKS ############################################################################### if [[ ! -d "$POD5_DIR" ]]; then echo "❌ POD5 directory not found:" echo "$POD5_DIR" pause_if_interactive exit 1 fi if [[ ! -f "$BARCODE_ARRANGEMENT" ]]; then echo "❌ Barcode arrangement TOML not found:" echo "$BARCODE_ARRANGEMENT" pause_if_interactive exit 1 fi if [[ ! -f "$BARCODE_SEQUENCES" ]]; then echo "❌ Barcode sequences FASTA not found:" echo "$BARCODE_SEQUENCES" pause_if_interactive exit 1 fi ############################################################################### # OUTPUT CHECKS ############################################################################### mkdir -p "$OUTPUT_DIR" if [[ -e "$OUT_BAM" ]]; then echo "❌ Output BAM already exists:" echo "$OUT_BAM" echo echo "Rename it, move it, or select another BAM filename." pause_if_interactive exit 1 fi if [[ -d "$DEMUX_DIR" ]] && [[ -n "$(find "$DEMUX_DIR" -mindepth 1 -print -quit 2>/dev/null)" ]]; then echo "❌ Demultiplexing folder is not empty:" echo "$DEMUX_DIR" echo echo "Rename it, move it, or select another folder name." pause_if_interactive exit 1 fi mkdir -p "$DEMUX_DIR" ############################################################################### # RUN INFORMATION ############################################################################### echo "🖥️ Architecture: $(uname -m)" echo echo "🧪 Conda environment:" echo "$CONDA_ENV" echo echo "🧬 Dorado executable:" echo "$DORADO" echo echo "🧬 Dorado version:" "$DORADO" --version echo echo "📂 POD5 input:" echo "$POD5_DIR" echo echo "📄 BAM output:" echo "$OUT_BAM" echo echo "📁 Demultiplexed FASTQ output:" echo "$DEMUX_DIR" ############################################################################### # BASECALL AND CLASSIFY CUSTOM BARCODES ############################################################################### echo echo "🧬 Basecalling and classifying custom barcodes..." ${basecallerCommand} ############################################################################### # DEMULTIPLEX THE ALREADY-CLASSIFIED BAM ############################################################################### echo echo "📂 Demultiplexing classified reads..." ${demuxCommand} ############################################################################### # COMPLETE ############################################################################### echo echo "✅ Basecalling and demultiplexing complete" echo echo "📄 BAM output:" echo "$OUT_BAM" echo echo "📁 FASTQ output:" echo "$DEMUX_DIR" ${pauseAtEnd ? "pause_if_interactive" : ""} `; } function buildTerminalCode() { const rawScript = buildRawCommandScript(); return `bash <<'DORADO_BASECALL_DEMUX'\n${rawScript}\nDORADO_BASECALL_DEMUX`; } ///////////////////////////////////////////////////////////////////////////// // UPDATE DISPLAY ///////////////////////////////////////////////////////////////////////////// function update() { const terminalCode = buildTerminalCode(); const issues = getIssues(); textarea.value = terminalCode; details.value = { terminalCode, commandFile: buildRawCommandScript() }; details.dispatchEvent( new Event("input", { bubbles: true }) ); if (issues.length > 0) { validation.style.background = "#fff4e5"; validation.style.border = "1px solid #e0a83e"; validation.style.color = "#6a4500"; validation.textContent = `⚠️ Fix before running:\n• ${issues.join( "\n• " )}`; copyButton.disabled = true; downloadButton.disabled = true; copyButton.style.cursor = "not-allowed"; downloadButton.style.cursor = "not-allowed"; copyButton.style.opacity = "0.55"; downloadButton.style.opacity = "0.55"; } else { validation.style.background = "#edf8ef"; validation.style.border = "1px solid #70b77e"; validation.style.color = "#175b26"; validation.textContent = "✅ Ready. Copied code can be pasted directly into macOS Terminal.\n" + `The script safely activates the Conda environment "${String( condaEnvironment.value || "" ).trim()}" before locating Dorado.`; copyButton.disabled = false; downloadButton.disabled = false; copyButton.style.cursor = "pointer"; downloadButton.style.cursor = "pointer"; copyButton.style.opacity = "1"; downloadButton.style.opacity = "1"; } } ///////////////////////////////////////////////////////////////////////////// // COPY BUTTON ///////////////////////////////////////////////////////////////////////////// copyButton.onclick = async () => { const issues = getIssues(); if (issues.length > 0) { return; } try { await navigator.clipboard.writeText(buildTerminalCode()); } catch { textarea.focus(); textarea.select(); document.execCommand("copy"); } copyButton.textContent = "✅ Copied!"; setTimeout(() => { copyButton.textContent = "📋 Copy Mac Terminal code"; }, 1500); }; ///////////////////////////////////////////////////////////////////////////// // DOWNLOAD BUTTON ///////////////////////////////////////////////////////////////////////////// downloadButton.onclick = () => { const issues = getIssues(); if (issues.length > 0) { return; } const blob = new Blob([buildRawCommandScript()], { type: "text/x-shellscript;charset=utf-8" }); const url = URL.createObjectURL(blob); const link = document.createElement("a"); link.href = url; link.download = safeDownloadName(scriptFilename.value); document.body.append(link); link.click(); link.remove(); setTimeout(() => URL.revokeObjectURL(url), 1000); downloadButton.textContent = "✅ Downloaded!"; setTimeout(() => { downloadButton.textContent = "💾 Download .command file"; }, 1500); }; ///////////////////////////////////////////////////////////////////////////// // EVENT LISTENERS ///////////////////////////////////////////////////////////////////////////// [ condaEnvironment, doradoExecutable, pod5Directory, outputDirectory, barcodeArrangement, barcodeSequences, model, kitName, minQscore, device, bamFilename, demuxFolderName, scriptFilename, options ].forEach((control) => { control.addEventListener("input", update); control.addEventListener("change", update); }); update(); return details; }32:T4cf0,viewof fastqConcatScriptMac = { ///////////////////////////////////////////////////////////////////////////// // INPUT CONTROLS ///////////////////////////////////////////////////////////////////////////// const inputPath = Inputs.text({ label: "📂 FASTQ folder path on the Mac", value: "", placeholder: "/Users/name/Desktop/Phage_580", style: "width:100%;" }); const outputFolderName = Inputs.text({ label: "📁 Output folder name", value: "Concatenated-FASTQ", placeholder: "Concatenated-FASTQ", style: "width:100%;" }); const recursiveInput = Inputs.toggle({ label: "🔁 Process subfolders and recreate their structure", value: true }); const overwriteInput = Inputs.toggle({ label: "♻️ Replace existing concatenated FASTQ files", value: false }); const pauseInput = Inputs.toggle({ label: "⏸️ Pause before a downloaded script closes", value: true }); const scriptFilename = Inputs.text({ label: "💾 Downloaded script filename", value: "concatenate_fastq_mac.command", placeholder: "concatenate_fastq_mac.command", style: "width:100%;" }); ///////////////////////////////////////////////////////////////////////////// // OUTPUT ELEMENTS ///////////////////////////////////////////////////////////////////////////// const textarea = html` `; const validation = html`

`; const copyButton = html` `; const downloadButton = html` `; ///////////////////////////////////////////////////////////////////////////// // LAYOUT ///////////////////////////////////////////////////////////////////////////// const instructions = html`

Enter an absolute Mac folder path beginning with /Users/, /Volumes/, or another /-based location.

The script concatenates folders containing at least two files with these extensions:

.fastq, .fq, .fastq.gz, and .fq.gz.

`; const controls = html`

`; controls.append( instructions, inputPath, outputFolderName, recursiveInput, overwriteInput, pauseInput, scriptFilename ); const buttonRow = html`

`; buttonRow.append(copyButton, downloadButton); controls.append(buttonRow, validation); const codePanel = html`

Generated macOS Terminal code

`; codePanel.append(textarea); const expandedContent = html`

`; expandedContent.append(controls, codePanel); const details = html`

🧬 Generate FASTQ concatenation code for macOS

`; details.append(expandedContent); ///////////////////////////////////////////////////////////////////////////// // HELPER FUNCTIONS ///////////////////////////////////////////////////////////////////////////// function shellQuote(value) { return `'${String(value ?? "").replace(/'/g, `'\\''`)}'`; } function safeDownloadName(value) { let name = String(value || "concatenate_fastq_mac.command") .trim() .replace(/[\\/:*?"<>|]/g, "_"); if (!name.toLowerCase().endsWith(".command")) { name += ".command"; } return name || "concatenate_fastq_mac.command"; } ///////////////////////////////////////////////////////////////////////////// // VALIDATION ///////////////////////////////////////////////////////////////////////////// function getIssues() { const issues = []; const folderPath = String(inputPath.value || "").trim(); const outputName = String(outputFolderName.value || "").trim(); if (!folderPath) { issues.push("Enter the folder containing the FASTQ files."); } else if (/^[A-Za-z]:[\\/]/.test(folderPath)) { issues.push( "The input is a Windows path. Enter a Mac path beginning with /." ); } else if (/^\/mnt\/[a-z]\//i.test(folderPath)) { issues.push("The input is a WSL path. Enter the corresponding Mac path."); } else if (!folderPath.startsWith("/")) { issues.push("The FASTQ folder must be an absolute Mac path."); } if (!outputName) { issues.push("Enter an output folder name."); } else if ( outputName.includes("/") || outputName.includes("\\") || outputName === "." || outputName === ".." ) { issues.push( "The output folder name cannot contain slashes or be . or ..." ); } if (!String(scriptFilename.value || "").trim()) { issues.push("Enter a downloaded script filename."); } return issues; } ///////////////////////////////////////////////////////////////////////////// // BASH SCRIPT GENERATOR ///////////////////////////////////////////////////////////////////////////// function buildBashScript() { const folderPath = String(inputPath.value || "").trim(); const outputName = String( outputFolderName.value || "Concatenated-FASTQ" ).trim(); const recursive = recursiveInput.value ? 1 : 0; const overwrite = overwriteInput.value ? 1 : 0; const pauseAtEnd = pauseInput.value ? 1 : 0; /* * Bash expressions beginning with ${ * are represented by __BASH_OPEN__. * * This prevents Observable JavaScript from interpreting them. */ const template = String.raw`#!/usr/bin/env bash set -Eeuo pipefail ############################################################################### # FUNCTIONS ############################################################################### pause_if_interactive() { if [[ -t 0 ]]; then echo read -r -p "Press Enter to close..." _ fi } on_error() { status=$? line=$1 echo echo "❌ Script failed at line $line (exit $status)" pause_if_interactive exit "$status" } trap 'on_error "$LINENO"' ERR ############################################################################### # USER SETTINGS ############################################################################### BASE_DIR=__BASE_DIR__ OUTPUT_FOLDER_NAME=__OUTPUT_FOLDER_NAME__ RECURSIVE=__RECURSIVE__ OVERWRITE=__OVERWRITE__ PAUSE_AT_END=__PAUSE_AT_END__ OUTPUT_ROOT="$BASE_DIR/$OUTPUT_FOLDER_NAME" ############################################################################### # SYSTEM CHECKS ############################################################################### if [[ "$(uname -s)" != "Darwin" ]]; then echo "❌ This script is intended for macOS." pause_if_interactive exit 1 fi for required_command in bash basename cat find gzip mkdir rm tr wc do if ! command -v "$required_command" >/dev/null 2>&1; then echo "❌ Required command not found: $required_command" pause_if_interactive exit 1 fi done ############################################################################### # INPUT CHECKS ############################################################################### if [[ ! -d "$BASE_DIR" ]]; then echo "❌ FASTQ folder not found:" echo "$BASE_DIR" pause_if_interactive exit 1 fi mkdir -p "$OUTPUT_ROOT" ############################################################################### # COUNTERS ############################################################################### processed_count=0 skipped_count=0 ############################################################################### # PROCESS ONE FOLDER ############################################################################### process_folder() { local folder="$1" local rel_path local dest_dir local parent_folder_name local out_file local file local count local line_count local all_gz=1 local any_gz=0 local files=() # Match common FASTQ extensions. # nocaseglob allows extensions such as .FASTQ or .FASTQ.GZ. shopt -s nullglob nocaseglob files=( "$folder"/*.fastq "$folder"/*.fq "$folder"/*.fastq.gz "$folder"/*.fq.gz ) shopt -u nullglob nocaseglob count=__BASH_OPEN__#files[@]} # Only concatenate folders containing at least two FASTQ files. if (( count < 2 )); then if (( count == 1 )); then echo "↪️ Skipping folder with only one FASTQ file:" echo " $folder" fi skipped_count=$((skipped_count + 1)) return 0 fi if [[ "$folder" == "$BASE_DIR" ]]; then rel_path="" dest_dir="$OUTPUT_ROOT" else rel_path="__BASH_OPEN__folder#"$BASE_DIR"/}" dest_dir="$OUTPUT_ROOT/$rel_path" fi parent_folder_name="$(basename "$folder")" mkdir -p "$dest_dir" # Determine whether the source files are compressed. for file in "__BASH_OPEN__files[@]}" do case "$file" in *.gz|*.GZ) any_gz=1 ;; *) all_gz=0 ;; esac done # If all files are compressed, retain gzip compression. # If the files are uncompressed or mixed, create an uncompressed FASTQ. if (( all_gz == 1 )); then out_file="$dest_dir/__BASH_OPEN__parent_folder_name}.fastq.gz" else out_file="$dest_dir/__BASH_OPEN__parent_folder_name}.fastq" fi echo echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━" echo "📁 Source folder:" echo " $folder" echo echo "🧬 FASTQ files found: $count" echo echo "📄 Output:" echo " $out_file" if [[ -e "$out_file" ]]; then if (( OVERWRITE == 1 )); then echo echo "♻️ Replacing existing output file." rm -f "$out_file" else echo echo "⚠️ Output already exists. Skipping this folder." echo " Enable overwrite or remove the existing file:" echo " $out_file" skipped_count=$((skipped_count + 1)) return 0 fi fi echo echo "➕ Concatenating files in filename order..." if (( all_gz == 1 )); then # Concatenated gzip members form a valid gzip stream. cat "__BASH_OPEN__files[@]}" > "$out_file" echo "🔍 Checking the concatenated gzip file..." gzip -t "$out_file" elif (( any_gz == 0 )); then # All source files are uncompressed. cat "__BASH_OPEN__files[@]}" > "$out_file" else # The folder contains both compressed and uncompressed FASTQ files. # Write a single uncompressed FASTQ output. : > "$out_file" for file in "__BASH_OPEN__files[@]}" do case "$file" in *.gz|*.GZ) gzip -cd "$file" >> "$out_file" ;; *) cat "$file" >> "$out_file" ;; esac done fi if [[ ! -s "$out_file" ]]; then echo "❌ The concatenated output file is empty:" echo "$out_file" return 1 fi # FASTQ records normally contain four lines each. # Check this for uncompressed output files. if [[ "$out_file" != *.gz ]]; then line_count=$( wc -l < "$out_file" | tr -d '[:space:]' ) if [[ -n "$line_count" ]] && (( line_count % 4 != 0 )); then echo echo "⚠️ Warning: the output contains $line_count lines." echo " This is not evenly divisible by four." echo " One or more input files may not be valid FASTQ." fi fi processed_count=$((processed_count + 1)) echo echo "✅ Concatenation complete:" echo " $out_file" } ############################################################################### # PROCESS FOLDERS ############################################################################### echo echo "🧬 FASTQ concatenation for macOS" echo "================================" echo echo "📂 Input root:" echo " $BASE_DIR" echo echo "📁 Output root:" echo " $OUTPUT_ROOT" if (( RECURSIVE == 1 )); then echo echo "🔁 Processing the input folder and all subfolders..." while IFS= read -r -d '' folder do # Never process the generated output directory. [[ "$folder" == "$OUTPUT_ROOT" ]] && continue process_folder "$folder" done < <( find "$BASE_DIR" \ -type d \ ! -path "$OUTPUT_ROOT" \ ! -path "$OUTPUT_ROOT/*" \ -print0 ) else echo echo "📄 Processing only the selected folder..." process_folder "$BASE_DIR" fi ############################################################################### # SUMMARY ############################################################################### echo echo "━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━" echo "🎉 FASTQ concatenation finished." echo echo "✅ Folders concatenated:" echo " $processed_count" echo echo "↪️ Folders skipped:" echo " $skipped_count" echo echo "📂 Output root:" echo " $OUTPUT_ROOT" if (( processed_count == 0 )); then echo echo "⚠️ No folders containing two or more FASTQ files were concatenated." fi if (( PAUSE_AT_END == 1 )); then pause_if_interactive fi `; return template .split("__BASH_OPEN__") .join("${") .split("__BASE_DIR__") .join(shellQuote(folderPath)) .split("__OUTPUT_FOLDER_NAME__") .join(shellQuote(outputName)) .split("__RECURSIVE__") .join(String(recursive)) .split("__OVERWRITE__") .join(String(overwrite)) .split("__PAUSE_AT_END__") .join(String(pauseAtEnd)); } ///////////////////////////////////////////////////////////////////////////// // MAC TERMINAL WRAPPER ///////////////////////////////////////////////////////////////////////////// function buildTerminalCode() { const bashScript = buildBashScript(); return `bash <<'FASTQ_CONCAT_MAC' ${bashScript} FASTQ_CONCAT_MAC`; } ///////////////////////////////////////////////////////////////////////////// // UPDATE DISPLAY ///////////////////////////////////////////////////////////////////////////// function update() { const issues = getIssues(); if (issues.length > 0) { textarea.value = ""; validation.style.background = "#fff4e5"; validation.style.border = "1px solid #e0a83e"; validation.style.color = "#6a4500"; validation.textContent = `⚠️ Fix before copying:\n• ${issues.join( "\n• " )}`; copyButton.disabled = true; downloadButton.disabled = true; copyButton.style.cursor = "not-allowed"; downloadButton.style.cursor = "not-allowed"; copyButton.style.opacity = "0.55"; downloadButton.style.opacity = "0.55"; } else { const terminalCode = buildTerminalCode(); textarea.value = terminalCode; validation.style.background = "#edf8ef"; validation.style.border = "1px solid #70b77e"; validation.style.color = "#175b26"; validation.textContent = "✅ The macOS script is ready.\n" + "Folders containing fewer than two FASTQ files will be skipped."; copyButton.disabled = false; downloadButton.disabled = false; copyButton.style.cursor = "pointer"; downloadButton.style.cursor = "pointer"; copyButton.style.opacity = "1"; downloadButton.style.opacity = "1"; } details.value = textarea.value; details.dispatchEvent( new Event("input", { bubbles: true }) ); } ///////////////////////////////////////////////////////////////////////////// // COPY BUTTON ///////////////////////////////////////////////////////////////////////////// copyButton.onclick = async () => { if (copyButton.disabled) { return; } try { await navigator.clipboard.writeText(textarea.value); } catch { textarea.focus(); textarea.select(); document.execCommand("copy"); } copyButton.textContent = "✅ Copied!"; setTimeout(() => { copyButton.textContent = "📋 Copy Mac Terminal code"; }, 1500); }; ///////////////////////////////////////////////////////////////////////////// // DOWNLOAD BUTTON ///////////////////////////////////////////////////////////////////////////// downloadButton.onclick = () => { if (downloadButton.disabled) { return; } const bashScript = buildBashScript(); const blob = new Blob([bashScript], { type: "text/x-shellscript;charset=utf-8" }); const url = URL.createObjectURL(blob); const link = document.createElement("a"); link.href = url; link.download = safeDownloadName(scriptFilename.value); document.body.append(link); link.click(); link.remove(); setTimeout(() => { URL.revokeObjectURL(url); }, 1000); downloadButton.textContent = "✅ Downloaded!"; setTimeout(() => { downloadButton.textContent = "💾 Download .command file"; }, 1500); }; ///////////////////////////////////////////////////////////////////////////// // EVENT LISTENERS ///////////////////////////////////////////////////////////////////////////// [ inputPath, outputFolderName, recursiveInput, overwriteInput, pauseInput, scriptFilename ].forEach((control) => { control.addEventListener("input", update); control.addEventListener("change", update); }); update(); return details; }33:T2fc5,viewof minimap2DehostScript = { const hostFastaInput = Inputs.text({ label: "🧬 Host genome FASTA (macOS path)", placeholder: "/Users/YourName/Desktop/host.fasta", style: "width: 600px" }); const readsFolderInput = Inputs.text({ label: "📁 Folder containing FASTQ files or sample subfolders", placeholder: "/Users/YourName/Desktop/Nanopore_Results", style: "width: 600px" }); const modeInput = Inputs.select( [ "One folder: combine FASTQs into one dehosted file", "Parse immediate subfolders separately" ], { label: "Search mode", value: "Parse immediate subfolders separately" } ); const envInput = Inputs.text({ label: "🧪 Conda environment", value: "reads-assembly-core", style: "width: 300px" }); const threadsInput = Inputs.number({ label: "🧵 Threads", value: 4, min: 1, max: 64 }); const textarea = html``; const copyBtn = html``; copyBtn.onclick = async () => { try { await navigator.clipboard.writeText(textarea.value); copyBtn.textContent = "✅ Copied!"; setTimeout(() => { copyBtn.textContent = "📋 Copy Mac Script code"; }, 1500); } catch (error) { copyBtn.textContent = "❌ Copy failed"; setTimeout(() => { copyBtn.textContent = "📋 Copy Mac Script code"; }, 1500); } }; function cleanMacPath(path) { let value = String(path ?? "").trim(); // Remove matching surrounding quotation marks. if ( (value.startsWith('"') && value.endsWith('"')) || (value.startsWith("'") && value.endsWith("'")) ) { value = value.slice(1, -1); } // Finder sometimes provides shell-escaped spaces when dragging paths. value = value.replace(/\\ /g, " "); return value; } function shQuote(value) { return `'${String(value).replace(/'/g, `'\\''`)}'`; } function generateScript() { const hostPath = cleanMacPath(hostFastaInput.value); const readsPath = cleanMacPath(readsFolderInput.value); const envName = envInput.value.trim() || "reads-assembly-core"; const threads = Math.max(1, Number.parseInt(threadsInput.value, 10) || 1); const parseSubfolders = modeInput.value === "Parse immediate subfolders separately"; if (!hostPath || !readsPath) { textarea.value = ""; copyBtn.disabled = true; return; } copyBtn.disabled = false; textarea.value = `bash <<'MINIMAP2_DEHOST' #!/usr/bin/env bash set -Eeuo pipefail pause_for_user() { echo echo "Press Enter to close..." read -r _ /dev/null 2>&1; then echo "🧪 Loading Conda using the shell hook..." eval "$(conda shell.bash hook)" else echo "❌ Conda could not be found." echo echo "Checked common locations including:" echo " /opt/miniconda3" echo " $HOME/miniconda3" echo " $HOME/miniconda" echo " /opt/anaconda3" echo " $HOME/anaconda3" pause_for_user exit 1 fi if ! conda env list | awk '{print $1}' | grep -Fxq "$ENV_NAME"; then echo "❌ Conda environment not found: $ENV_NAME" echo echo "Available environments:" conda env list pause_for_user exit 1 fi echo echo "🧪 Activating Conda environment: $ENV_NAME" conda activate "$ENV_NAME" # ------------------------------------------------------------ # Check required programs and input paths # ------------------------------------------------------------ for tool in minimap2 samtools; do if ! command -v "$tool" >/dev/null 2>&1; then echo "❌ Required program not found: $tool" echo echo "Install it in the environment with:" echo " conda install -n \\"$ENV_NAME\\" -c conda-forge -c bioconda $tool" pause_for_user exit 1 fi done echo echo "minimap2: $(command -v minimap2)" echo "samtools: $(command -v samtools)" echo if [ ! -f "$HOST_FASTA" ]; then echo "❌ Host FASTA was not found:" echo " $HOST_FASTA" pause_for_user exit 1 fi if [ ! -d "$READS_DIR" ]; then echo "❌ Reads folder was not found:" echo " $READS_DIR" pause_for_user exit 1 fi # ------------------------------------------------------------ # Prepare output folder and host index # ------------------------------------------------------------ OUT_DIR="$READS_DIR/dehosted_output" mkdir -p "$OUT_DIR" HOST_FILENAME="$(basename "$HOST_FASTA")" HOST_STEM="\${HOST_FILENAME%.*}" INDEX="$OUT_DIR/\${HOST_STEM}.mmi" if [ ! -f "$INDEX" ] || [ "$HOST_FASTA" -nt "$INDEX" ]; then echo "📦 Creating Minimap2 host index..." minimap2 \\ -t "$THREADS" \\ -d "$INDEX" \\ "$HOST_FASTA" echo "✅ Host index created:" echo " $INDEX" else echo "ℹ️ Using existing host index:" echo " $INDEX" fi # ------------------------------------------------------------ # Function to dehost one folder # ------------------------------------------------------------ dehost_folder() { local input_folder="$1" local output_folder="$2" local sample="$3" local -a fq_files=() local f local out_fastq local partial_fastq local log_file mkdir -p "$output_folder" # Replace spaces in the sample name with underscores. sample="\${sample// /_}" if [ -z "$sample" ]; then sample="sample" fi # macOS ships with Bash 3.2, which does not provide mapfile. # Shell globbing is used instead. shopt -s nullglob shopt -s nocaseglob for f in \\ "$input_folder"/*.fastq \\ "$input_folder"/*.fq \\ "$input_folder"/*.fastq.gz \\ "$input_folder"/*.fq.gz do if [ -f "$f" ]; then fq_files+=("$f") fi done shopt -u nocaseglob shopt -u nullglob if (( \${#fq_files[@]} == 0 )); then echo echo "⚠ No FASTQ files found in:" echo " $input_folder" return 0 fi out_fastq="$output_folder/NoHost_\${sample}.fastq" partial_fastq="\${out_fastq}.partial" log_file="$output_folder/\${sample}_minimap2.log" echo echo "----------------------------------------------" echo "Sample: $sample" echo "----------------------------------------------" echo "📁 Input folder:" echo " $input_folder" echo echo "📁 Output folder:" echo " $output_folder" echo echo "✅ Found \${#fq_files[@]} FASTQ file(s):" for f in "\${fq_files[@]}"; do echo " + $(basename "$f")" done rm -f "$partial_fastq" echo echo "🧬 Aligning reads against the host genome..." echo "🧹 Retaining only reads that do not map to the host..." # Minimap2 can stream multiple FASTQ and FASTQ.GZ files directly. # This avoids creating a large temporary combined FASTQ file. if ! minimap2 \\ -ax map-ont \\ --secondary=no \\ -t "$THREADS" \\ "$INDEX" \\ "\${fq_files[@]}" \\ 2> "$log_file" | samtools view \\ -u \\ -f 4 \\ - | samtools fastq \\ -n \\ - \\ > "$partial_fastq" then rm -f "$partial_fastq" echo echo "❌ Dehosting failed for sample: $sample" echo "Minimap2 log:" echo " $log_file" return 1 fi mv "$partial_fastq" "$out_fastq" if [ ! -s "$out_fastq" ]; then echo echo "⚠ The output FASTQ is empty." echo "All reads may have mapped to the host, or the input files may be empty." else output_lines="$(wc -l < "$out_fastq" | tr -d ' ')" output_reads=$((output_lines / 4)) echo echo "✅ Dehosted FASTQ created:" echo " $out_fastq" echo echo "📊 Reads retained: $output_reads" fi echo "📝 Minimap2 log:" echo " $log_file" } # ------------------------------------------------------------ # Process the selected folder structure # ------------------------------------------------------------ if [ "$PARSE_SUBFOLDERS" -eq 1 ]; then echo echo "🔁 Processing immediate subfolders separately..." found_folder=0 for folder in "$READS_DIR"/*/; do [ -d "$folder" ] || continue folder_clean="\${folder%/}" sample="$(basename "$folder_clean")" # Skip the output folder if the script is run again. if [ "$folder_clean" = "$OUT_DIR" ]; then continue fi found_folder=1 dehost_folder \\ "$folder_clean" \\ "$OUT_DIR/$sample" \\ "$sample" done if [ "$found_folder" -eq 0 ]; then echo echo "⚠ No immediate subfolders were found under:" echo " $READS_DIR" echo echo "When FASTQ files are directly inside the selected folder," echo "choose:" echo " One folder: combine FASTQs into one dehosted file" fi else echo echo "📄 Processing FASTQ files directly inside the selected folder..." sample="$(basename "$READS_DIR")" dehost_folder \\ "$READS_DIR" \\ "$OUT_DIR" \\ "$sample" fi echo echo "==============================================" echo "🎉 Finished removing host reads" echo "==============================================" echo echo "📁 Main output folder:" echo " $OUT_DIR" pause_for_user MINIMAP2_DEHOST `; } hostFastaInput.addEventListener("input", generateScript); readsFolderInput.addEventListener("input", generateScript); modeInput.addEventListener("input", generateScript); envInput.addEventListener("input", generateScript); threadsInput.addEventListener("input", generateScript); generateScript(); return html`

⬇ Minimap2 host-read removal — macOS

${hostFastaInput} ${readsFolderInput} ${modeInput} ${envInput} ${threadsInput}

Copy the generated code and paste it directly into macOS Terminal.

${copyBtn}

${textarea}

`; }34:T5e28,viewof runNanoCompFromBarcodeMapMac = { const folderInput = Inputs.text({ label: "📂 Mac FASTQ parent folder", value: "", placeholder: "/Users/name/Desktop/Nanopore_Results/fastq_pass", style: "width:100%;" }); const csvInput = Inputs.text({ label: "📄 Optional CSV — Column A = Barcode, Column B = Phage Name", value: "", placeholder: "/Users/name/Desktop/barcode_to_phage.csv", style: "width:100%;" }); const useFolderNamesInput = Inputs.checkbox( ["Use folder name for sample names instead of CSV"], { label: "Sample naming", value: [] } ); const recursiveInput = Inputs.checkbox( ["Search all nested subfolders for FASTQ files"], { label: "Search options", value: ["Search all nested subfolders for FASTQ files"] } ); const condaEnvironmentInput = Inputs.text({ label: "🧪 Conda environment", value: "reads-assembly-core", style: "width:100%;" }); const outputFolderInput = Inputs.text({ label: "📁 NanoComp output folder name", value: "nanocomp_output", style: "width:100%;" }); const threadsInput = Inputs.range([1, 32], { label: "Threads", value: 4, step: 1 }); const replaceOutputInput = Inputs.toggle({ label: "♻️ Replace an existing non-empty output folder", value: false }); const pauseInput = Inputs.toggle({ label: "⏸️ Pause before a downloaded .command file closes", value: true }); const scriptFilenameInput = Inputs.text({ label: "💾 Downloaded script filename", value: "run_nanocomp_mac.command", style: "width:100%;" }); const help = html`

Use absolute Mac paths beginning with /Users/ or /Volumes/.

Supported files: .fastq, .fq, .fastq.gz, and .fq.gz.

CSV example:

barcode001,Olympi
barcode002,Tadpole
barcode003,Seldom

The script matches the barcode text or barcode number to the FASTQ parent-folder or filename.

`; const scriptArea = html``; const validation = html`

`; const copyButton = html``; const downloadButton = html``; const controls = html`

`; controls.append( help, folderInput, csvInput, useFolderNamesInput, recursiveInput, condaEnvironmentInput, outputFolderInput, threadsInput, replaceOutputInput, pauseInput, scriptFilenameInput ); const buttons = html`

`; buttons.append(copyButton, downloadButton); controls.append(buttons, validation); const codePanel = html`

Generated macOS Terminal code

`; codePanel.append(scriptArea); const content = html`

`; content.append(controls, codePanel); const details = html`

🧬 Generate NanoComp code for macOS

`; details.append(content); function shellQuote(value) { return `'${String(value ?? "").replace(/'/g, `'\\''`)}'`; } function selected(control, label) { return Array.isArray(control.value) && control.value.includes(label); } function safeDownloadName(value) { let name = String(value || "run_nanocomp_mac.command") .trim() .replace(/[\\/:*?"<>|]/g, "_"); if (!name.toLowerCase().endsWith(".command")) { name += ".command"; } return name || "run_nanocomp_mac.command"; } function getIssues() { const issues = []; const folder = String(folderInput.value || "").trim(); const csv = String(csvInput.value || "").trim(); const env = String(condaEnvironmentInput.value || "").trim(); const output = String(outputFolderInput.value || "").trim(); if (!folder) { issues.push("Enter the Mac FASTQ parent folder."); } else if ( /^[A-Za-z]:[\\/]/.test(folder) || /^\/mnt\/[a-z]\//i.test(folder) ) { issues.push( "The FASTQ folder is a Windows or WSL path. Enter a Mac path." ); } else if (!folder.startsWith("/")) { issues.push("The FASTQ folder must be an absolute Mac path."); } if (csv) { if (/^[A-Za-z]:[\\/]/.test(csv) || /^\/mnt\/[a-z]\//i.test(csv)) { issues.push("The CSV is a Windows or WSL path. Enter a Mac path."); } else if (!csv.startsWith("/")) { issues.push("The CSV must be an absolute Mac path."); } } if (!/^[A-Za-z0-9._-]+$/.test(env)) { issues.push( "The Conda environment name contains unsupported characters." ); } if ( !output || output.includes("/") || output.includes("\\") || output === "." || output === ".." ) { issues.push("Enter an output folder name without slashes."); } if (!String(scriptFilenameInput.value || "").trim()) { issues.push("Enter a downloaded script filename."); } return issues; } function buildBashScript() { const folder = String(folderInput.value || "").trim(); const csv = String(csvInput.value || "").trim(); const env = String( condaEnvironmentInput.value || "reads-assembly-core" ).trim(); const output = String(outputFolderInput.value || "nanocomp_output").trim(); const useFolderNames = selected( useFolderNamesInput, "Use folder name for sample names instead of CSV" ) || !csv; const recursive = selected( recursiveInput, "Search all nested subfolders for FASTQ files" ); const threads = Number.isFinite(Number(threadsInput.value)) ? Math.max(1, Math.round(Number(threadsInput.value))) : 4; /* * Bash expressions beginning with ${ * are temporarily written as __BASH_OPEN__. * * This prevents Observable from interpreting * Bash parameter expansion as JavaScript. */ const template = String.raw`#!/usr/bin/env bash set -Eeo pipefail pause_if_interactive() { if [[ -t 0 ]]; then echo read -r -p "Press Enter to close..." _ fi } on_error() { status=$? echo echo "❌ Script failed at line $1 (exit $status)" pause_if_interactive exit "$status" } trap 'on_error "$LINENO"' ERR ############################################################################### # USER SETTINGS ############################################################################### INPUT_DIR=__INPUT_DIR__ CSV_MAP=__CSV_MAP__ CONDA_ENV=__CONDA_ENV__ OUTPUT_FOLDER_NAME=__OUTPUT_FOLDER__ USE_FOLDER_NAMES=__USE_FOLDER_NAMES__ RECURSIVE=__RECURSIVE__ THREADS=__THREADS__ REPLACE_OUTPUT=__REPLACE_OUTPUT__ PAUSE_AT_END=__PAUSE_AT_END__ OUTPUT_DIR="$INPUT_DIR/$OUTPUT_FOLDER_NAME" ############################################################################### # MACOS CHECK ############################################################################### if [[ "$(uname -s)" != "Darwin" ]]; then echo "❌ This script is intended for macOS." pause_if_interactive exit 1 fi for cmd in \ awk \ basename \ dirname \ find \ grep \ ls \ sed \ tr do if ! command -v "$cmd" >/dev/null 2>&1; then echo "❌ Required command not found: $cmd" pause_if_interactive exit 1 fi done ############################################################################### # LOCATE CONDA ############################################################################### echo echo "🔎 Locating Conda..." CONDA_SH="" if command -v conda >/dev/null 2>&1; then CONDA_BASE=$( conda info --base 2>/dev/null || true ) if [[ -n "$CONDA_BASE" ]] && [[ -f "$CONDA_BASE/etc/profile.d/conda.sh" ]]; then CONDA_SH="$CONDA_BASE/etc/profile.d/conda.sh" fi fi if [[ -z "$CONDA_SH" ]]; then for base in \ /opt/miniconda3 \ /opt/miniforge3 \ /opt/anaconda3 \ "$HOME/miniconda3" \ "$HOME/miniforge3" \ "$HOME/anaconda3" \ "$HOME/mambaforge" \ "$HOME/miniconda" do if [[ -f "$base/etc/profile.d/conda.sh" ]]; then CONDA_SH="$base/etc/profile.d/conda.sh" break fi done fi if [[ -z "$CONDA_SH" ]]; then echo "❌ Conda could not be found." pause_if_interactive exit 1 fi ############################################################################### # ACTIVATE CONDA ENVIRONMENT ############################################################################### # Conda hook scripts may reference optional variables during activation. set +u . "$CONDA_SH" if ! conda activate "$CONDA_ENV"; then echo "❌ Failed to activate Conda environment:" echo " $CONDA_ENV" echo conda env list || true pause_if_interactive exit 1 fi if [[ -z "__BASH_OPEN__CONDA_PREFIX:-}" ]]; then echo "❌ CONDA_PREFIX is empty after activation." pause_if_interactive exit 1 fi echo "✅ Active environment: $CONDA_ENV" echo " $CONDA_PREFIX" ############################################################################### # CHECK NANOCOMP ############################################################################### if ! command -v NanoComp >/dev/null 2>&1; then echo "❌ NanoComp was not found in:" echo " $CONDA_ENV" echo echo "Install it with:" echo " conda activate $CONDA_ENV" echo " conda install -c bioconda nanocomp" pause_if_interactive exit 1 fi echo echo "🧬 NanoComp version:" NanoComp --version 2>&1 || true ############################################################################### # CHECK INPUTS ############################################################################### if [[ ! -d "$INPUT_DIR" ]]; then echo "❌ FASTQ parent folder not found:" echo " $INPUT_DIR" pause_if_interactive exit 1 fi if [[ "$USE_FOLDER_NAMES" == "false" ]]; then if [[ -z "$CSV_MAP" ]] || [[ ! -f "$CSV_MAP" ]]; then echo "❌ CSV mapping file not found:" echo " $CSV_MAP" pause_if_interactive exit 1 fi fi ############################################################################### # CHECK OUTPUT ############################################################################### if [[ -d "$OUTPUT_DIR" ]] && [[ -n "$(ls -A "$OUTPUT_DIR" 2>/dev/null)" ]]; then if (( REPLACE_OUTPUT == 1 )); then echo "♻️ Removing existing output folder:" echo " $OUTPUT_DIR" rm -rf "$OUTPUT_DIR" else echo "❌ Output folder already exists and is not empty:" echo " $OUTPUT_DIR" echo echo "Enable replacement or choose another output folder." pause_if_interactive exit 1 fi fi mkdir -p "$OUTPUT_DIR" ############################################################################### # ARRAYS ############################################################################### all_fastq_files=() fastq_files=() sample_names=() seen_files=() seen_names=() ############################################################################### # HELPER FUNCTIONS ############################################################################### array_contains() { local target="$1" shift local item for item in "$@" do if [[ "$item" == "$target" ]]; then return 0 fi done return 1 } clean_name() { local value="$1" value="__BASH_OPEN__value#$'\xEF\xBB\xBF'}" value="__BASH_OPEN__value//$'\r'/}" printf '%s' "$value" | sed 's/^[[:space:]]*//;s/[[:space:]]*$//' } barcode_number() { local value="$1" local number number=$( printf '%s' "$value" | grep -oE '[0-9]+' | tail -n1 || true ) if [[ -z "$number" ]]; then printf '%s' "" return 0 fi number=$( printf '%s' "$number" | sed 's/^0*//' ) if [[ -z "$number" ]]; then number="0" fi printf '%s' "$number" } add_sample() { local file="$1" local name="$2" if [[ -z "$file" ]] || [[ -z "$name" ]]; then return 0 fi if array_contains \ "$file" \ "__BASH_OPEN__seen_files[@]}" then echo "⚠️ Skipping duplicate FASTQ:" echo " $file" return 0 fi if array_contains \ "$name" \ "__BASH_OPEN__seen_names[@]}" then echo "⚠️ Skipping duplicate sample name: $name" echo " $file" return 0 fi fastq_files+=("$file") sample_names+=("$name") seen_files+=("$file") seen_names+=("$name") echo "✅ Added: $name" echo " $file" } ############################################################################### # FIND FASTQ FILES ############################################################################### collect_fastq_files() { local file local sample_dir all_fastq_files=() if [[ "$RECURSIVE" == "true" ]]; then while IFS= read -r -d '' file do all_fastq_files+=("$file") done < <( find "$INPUT_DIR" \ -type f \ $ \ -iname '*.fastq' -o \ -iname '*.fastq.gz' -o \ -iname '*.fq' -o \ -iname '*.fq.gz' \ $ \ ! -path "$OUTPUT_DIR" \ ! -path "$OUTPUT_DIR/*" \ -print0 ) else shopt -s nullglob nocaseglob for sample_dir in "$INPUT_DIR"/* do [[ -d "$sample_dir" ]] || continue [[ "$sample_dir" == "$OUTPUT_DIR" ]] && continue for file in \ "$sample_dir"/*.fastq \ "$sample_dir"/*.fastq.gz \ "$sample_dir"/*.fq \ "$sample_dir"/*.fq.gz do if [[ -f "$file" ]]; then all_fastq_files+=("$file") fi done done shopt -u nullglob nocaseglob fi } collect_fastq_files echo echo "🔎 FASTQ files discovered: __BASH_OPEN__#all_fastq_files[@]}" if (( __BASH_OPEN__#all_fastq_files[@]} == 0 )); then echo "❌ No FASTQ files were found under:" echo " $INPUT_DIR" pause_if_interactive exit 1 fi ############################################################################### # CREATE SAMPLE LIST ############################################################################### if [[ "$USE_FOLDER_NAMES" == "true" ]]; then echo echo "📁 Using parent-folder names for sample names..." for file in "__BASH_OPEN__all_fastq_files[@]}" do sample_name=$( basename "$( dirname "$file" )" ) add_sample \ "$file" \ "$sample_name" done else echo echo "📄 Using the CSV barcode-to-sample map..." while IFS=, read -r barcode sample extra || [[ -n "$barcode$sample$extra" ]] do barcode=$( clean_name "$barcode" ) sample=$( clean_name "$sample" ) if [[ -z "$barcode" ]] || [[ -z "$sample" ]]; then continue fi barcode_lc=$( printf '%s' "$barcode" | tr '[:upper:]' '[:lower:]' ) sample_lc=$( printf '%s' "$sample" | tr '[:upper:]' '[:lower:]' ) if [[ "$barcode_lc" == "barcode" ]] || [[ "$sample_lc" == "phage" ]] || [[ "$sample_lc" == "phage name" ]] || [[ "$sample_lc" == "sample" ]] || [[ "$sample_lc" == "sample name" ]]; then continue fi csv_number=$( barcode_number "$barcode" ) if [[ -z "$csv_number" ]]; then echo "⚠️ No barcode number found in CSV entry:" echo " $barcode" continue fi found_file="" ########################################################################### # FIRST TRY A DIRECT BARCODE TEXT MATCH ########################################################################### for file in "__BASH_OPEN__all_fastq_files[@]}" do folder=$( basename "$( dirname "$file" )" ) filename=$( basename "$file" ) folder_lc=$( printf '%s' "$folder" | tr '[:upper:]' '[:lower:]' ) filename_lc=$( printf '%s' "$filename" | tr '[:upper:]' '[:lower:]' ) if [[ "$folder_lc" == *"$barcode_lc"* ]] || [[ "$filename_lc" == *"$barcode_lc"* ]]; then found_file="$file" break fi done ########################################################################### # THEN TRY A NUMERIC BARCODE MATCH ########################################################################### if [[ -z "$found_file" ]]; then for file in "__BASH_OPEN__all_fastq_files[@]}" do folder=$( basename "$( dirname "$file" )" ) filename=$( basename "$file" ) folder_number=$( barcode_number "$folder" ) file_number=$( barcode_number "$filename" ) if [[ "$folder_number" == "$csv_number" ]] || [[ "$file_number" == "$csv_number" ]]; then found_file="$file" break fi done fi if [[ -n "$found_file" ]]; then add_sample \ "$found_file" \ "$sample" else echo "⚠️ No FASTQ matched CSV barcode:" echo " $barcode" fi done < "$CSV_MAP" fi ############################################################################### # VERIFY MATCHED SAMPLES ############################################################################### echo echo "Matched FASTQ samples: __BASH_OPEN__#fastq_files[@]}" if (( __BASH_OPEN__#fastq_files[@]} < 2 )); then echo "❌ NanoComp requires at least two matched FASTQ samples." pause_if_interactive exit 1 fi if (( __BASH_OPEN__#fastq_files[@]} != __BASH_OPEN__#sample_names[@]} )); then echo "❌ FASTQ and sample-name counts do not match." pause_if_interactive exit 1 fi echo echo "Files to compare:" index=0 while (( index < __BASH_OPEN__#fastq_files[@]} )) do echo " - __BASH_OPEN__sample_names[$index]}" echo " __BASH_OPEN__fastq_files[$index]}" index=$((index + 1)) done ############################################################################### # RUN NANOCOMP ############################################################################### echo echo "🧬 Running NanoComp..." echo "Output:" echo " $OUTPUT_DIR" echo "Threads:" echo " $THREADS" NanoComp \ --fastq "__BASH_OPEN__fastq_files[@]}" \ -n "__BASH_OPEN__sample_names[@]}" \ -o "$OUTPUT_DIR" \ -t "$THREADS" ############################################################################### # COMPLETE ############################################################################### echo echo "✅ NanoComp completed successfully." echo "📁 Results:" echo " $OUTPUT_DIR" if (( PAUSE_AT_END == 1 )); then pause_if_interactive fi `; return template .split("__BASH_OPEN__") .join("${") .split("__INPUT_DIR__") .join(shellQuote(folder)) .split("__CSV_MAP__") .join(shellQuote(csv)) .split("__CONDA_ENV__") .join(shellQuote(env)) .split("__OUTPUT_FOLDER__") .join(shellQuote(output)) .split("__USE_FOLDER_NAMES__") .join(useFolderNames ? "true" : "false") .split("__RECURSIVE__") .join(recursive ? "true" : "false") .split("__THREADS__") .join(String(threads)) .split("__REPLACE_OUTPUT__") .join(replaceOutputInput.value ? "1" : "0") .split("__PAUSE_AT_END__") .join(pauseInput.value ? "1" : "0"); } function buildTerminalCode() { return `bash <<'NANOCOMP_MAC' ${buildBashScript()} NANOCOMP_MAC`; } function setButtonsEnabled(enabled) { copyButton.disabled = !enabled; downloadButton.disabled = !enabled; copyButton.style.opacity = enabled ? "1" : "0.55"; downloadButton.style.opacity = enabled ? "1" : "0.55"; copyButton.style.cursor = enabled ? "pointer" : "not-allowed"; downloadButton.style.cursor = enabled ? "pointer" : "not-allowed"; } function update() { const issues = getIssues(); if (issues.length) { scriptArea.value = ""; validation.style.background = "#fff4e5"; validation.style.border = "1px solid #e0a83e"; validation.style.color = "#6a4500"; validation.textContent = `⚠️ Fix before copying:\n• ${issues.join( "\n• " )}`; setButtonsEnabled(false); } else { const useFolderNames = selected( useFolderNamesInput, "Use folder name for sample names instead of CSV" ) || !String(csvInput.value || "").trim(); scriptArea.value = buildTerminalCode(); validation.style.background = "#edf8ef"; validation.style.border = "1px solid #70b77e"; validation.style.color = "#175b26"; validation.textContent = "✅ The macOS NanoComp script is ready.\n" + (useFolderNames ? "Sample names will come from FASTQ parent-folder names." : "Sample names will come from the barcode CSV."); setButtonsEnabled(true); } details.value = scriptArea.value; details.dispatchEvent( new Event("input", { bubbles: true }) ); } copyButton.onclick = async () => { if (copyButton.disabled) { return; } try { await navigator.clipboard.writeText(scriptArea.value); } catch { scriptArea.focus(); scriptArea.select(); document.execCommand("copy"); } copyButton.textContent = "✅ Copied!"; setTimeout(() => { copyButton.textContent = "📋 Copy Mac Terminal code"; }, 1500); }; downloadButton.onclick = () => { if (downloadButton.disabled) { return; } const blob = new Blob([buildBashScript()], { type: "text/x-shellscript;charset=utf-8" }); const url = URL.createObjectURL(blob); const link = document.createElement("a"); link.href = url; link.download = safeDownloadName(scriptFilenameInput.value); document.body.append(link); link.click(); link.remove(); setTimeout(() => URL.revokeObjectURL(url), 1000); downloadButton.textContent = "✅ Downloaded!"; setTimeout(() => { downloadButton.textContent = "💾 Download .command file"; }, 1500); }; [ folderInput, csvInput, useFolderNamesInput, recursiveInput, condaEnvironmentInput, outputFolderInput, threadsInput, replaceOutputInput, pauseInput, scriptFilenameInput ].forEach((control) => { control.addEventListener("input", update); control.addEventListener("change", update); }); update(); return details; }35:T479c,viewof filtlongConfigurator = { const folderPathInput = Inputs.text({ label: "📁 Path to parent folder containing FASTQ files or subfolders (macOS-style)", placeholder: "/Users/YourName/Desktop/Nanopore_Results/Run1/Demux_Output", style: "width: 600px" }); const envInput = Inputs.text({ label: "🧪 Conda environment", value: "reads-assembly-core", style: "width: 320px" }); const iterateSubfoldersInput = Inputs.toggle({ label: "🔁 Iterate immediate subfolders of parent folder", value: true }); const dedupeInput = Inputs.toggle({ label: "🧹 Remove duplicate read names before Filtlong", value: true }); const minReadLengthInput = Inputs.number({ label: "📏 Minimum read length (bp)", value: 200, min: 50, max: 10000, step: 50, style: "width: 300px" }); const minAccuracyInput = Inputs.number({ label: "🎯 Minimum mean read accuracy (%) (--min_mean_q)", value: 99, min: 0, max: 99.9999, step: 0.1, style: "width: 300px" }); const qualityInfo = html`

`; const targetBasesInput = Inputs.text({ label: "🧮 Maximum bases (--target_bases) — leave blank to omit", placeholder: "6000000", style: "width: 300px" }); const textarea = html``; const buttonStyle = ` padding: 0.5em 0.85em; border: 1px solid #bbb; border-radius: 6px; background: #f7f7f7; cursor: pointer; font-size: 0.9em; `; const copyBtn = html``; const status = html``; function shQuote(value) { return `'${String(value).replace(/'/g, `'\\''`)}'`; } function normalizeMacPath(value) { let path = String(value ?? "").trim(); if ( (path.startsWith('"') && path.endsWith('"')) || (path.startsWith("'") && path.endsWith("'")) ) { path = path.slice(1, -1); } // Convert paths copied from Terminal with escaped spaces. path = path.replace(/\\ /g, " "); return path; } function numberOrFallback(value, fallback) { if (value === null || value === undefined || value === "") { return fallback; } const number = Number(value); return Number.isFinite(number) ? number : fallback; } function formatNumber(value, decimalPlaces = 4) { const number = Number(value); if (!Number.isFinite(number)) { return ""; } return Number(number.toFixed(decimalPlaces)).toString(); } function accuracyToQ(accuracyPercent) { const accuracy = Number(accuracyPercent); if (!Number.isFinite(accuracy) || accuracy <= 0) { return 0; } if (accuracy >= 100) { return Infinity; } const errorProbability = 1 - accuracy / 100; return -10 * Math.log10(errorProbability); } function formatQ(value) { if (!Number.isFinite(value)) { return "∞"; } if (Math.abs(value - Math.round(value)) < 0.005) { return String(Math.round(value)); } return value.toFixed(1); } function filenameToken(value) { return String(value) .replace(/\./g, "p") .replace(/[^A-Za-z0-9_-]/g, ""); } function formatMB(value) { const number = Number(value); if (!Number.isFinite(number) || number <= 0) { return null; } const megabases = number / 1_000_000; return Number.isInteger(megabases) ? `${megabases}Mb` : `${megabases.toFixed(1)}Mb`; } function generateCommand() { const minLength = Math.round( numberOrFallback(minReadLengthInput.value, 200) ); const rawAccuracy = numberOrFallback(minAccuracyInput.value, 99); const minAccuracy = Math.min(99.9999, Math.max(0, rawAccuracy)); const minAccuracyText = formatNumber(minAccuracy); const equivalentQ = accuracyToQ(minAccuracy); const qDisplay = formatQ(equivalentQ); qualityInfo.innerHTML = ` Equivalent Phred threshold: approximately Q${qDisplay}
90% = Q10 • 99% = Q20 • 99.9% = Q30

Filtlong expects percent accuracy for --min_mean_q, not a Phred Q-score.

`; const envName = envInput.value.trim() || "reads-assembly-core"; const macPath = normalizeMacPath(folderPathInput.value); const iterateSubfolders = Boolean(iterateSubfoldersInput.value); const dedupeReads = Boolean(dedupeInput.value); const targetBasesRaw = String(targetBasesInput.value ?? "").trim(); const targetBases = Number(targetBasesRaw); const hasValidTargetBases = targetBasesRaw !== "" && Number.isFinite(targetBases) && targetBases > 0; const mbFormatted = hasValidTargetBases ? formatMB(targetBases) : null; if (!macPath) { textarea.value = ""; copyBtn.disabled = true; return; } copyBtn.disabled = false; const accuracyToken = filenameToken(minAccuracyText); const qToken = filenameToken(qDisplay); const baseFolderName = `FiltLong_MinRead-${minLength}bp_Acc-${accuracyToken}pct_Q${qToken}`; const outputFolderName = hasValidTargetBases && mbFormatted ? `${baseFolderName}_Bases-${mbFormatted}` : baseFolderName; const filtlongParams = [ `--min_length ${minLength}`, `--min_mean_q ${minAccuracyText}` ]; if (hasValidTargetBases) { filtlongParams.unshift(`--target_bases ${Math.round(targetBases)}`); } const filtlongParameterLines = filtlongParams.join(" \\\n "); textarea.value = `bash <<'FILTLONG_SCRIPT' #!/usr/bin/env bash set -Eeuo pipefail BASE_DIR_INPUT=${shQuote(macPath)} ENV_NAME=${shQuote(envName)} ITERATE_SUBFOLDERS=${iterateSubfolders ? "1" : "0"} DEDUPLICATE_READS=${dedupeReads ? "1" : "0"} OUTPUT_FOLDER_NAME=${shQuote(outputFolderName)} CONDA_EXE="" FILTLONG_PATH="" CURRENT_TMP="" cleanup() { if [ -n "$CURRENT_TMP" ] && [ -f "$CURRENT_TMP" ]; then rm -f "$CURRENT_TMP" fi } on_error() { local status=$? trap - ERR echo echo "ERROR: Filtlong script failed at line $1." echo "Exit status: $status" cleanup echo echo "Press Enter to close..." read -r _ /dev/null 2>&1; then echo echo "ERROR: Conda environment was not found:" echo " $ENV_NAME" echo echo "Available Conda environments:" "$CONDA_EXE" env list echo echo "Press Enter to close..." read -r _ /dev/null | /usr/bin/awk 'NF {last=$0} END {print last}' | /usr/bin/tr -d '\\r' || true )" if [ -z "$FILTLONG_PATH" ] || [ ! -x "$FILTLONG_PATH" ]; then echo echo "ERROR: Filtlong was not found in environment:" echo " $ENV_NAME" echo echo "Install or reinstall Filtlong, then run this script again." echo echo "Verification command:" echo " $CONDA_EXE run -n $ENV_NAME which filtlong" echo echo "Press Enter to close..." read -r _ /dev/null 2>&1 || HELP_STATUS=$? if [ "$HELP_STATUS" -gt 1 ]; then echo echo "ERROR: Filtlong was found but did not run correctly." echo "Exit status: $HELP_STATUS" echo echo "Press Enter to close..." read -r _ "$output" } process_folder() { local folder="$1" local folder_name="" local out_dir="" folder_name="$(basename "$folder")" out_dir="$PARENT_OUT_DIR/$folder_name" mkdir -p "$out_dir" shopt -s nullglob local files=( "$folder"/*.fastq "$folder"/*.fq ) shopt -u nullglob if (( \${#files[@]} == 0 )); then echo echo "WARNING: No .fastq or .fq files found in:" echo " $folder" return 0 fi echo echo "------------------------------------------------------------" echo "Processing folder:" echo " $folder" echo echo "Output folder:" echo " $out_dir" echo "------------------------------------------------------------" for file in "\${files[@]}"; do local filename="" local output_file="" local input_for_filtlong="" local input_size="" local output_size="" filename="$(basename "$file")" output_file="$out_dir/filtered_$filename" echo echo "Input file:" echo " $filename" if [ "$DEDUPLICATE_READS" -eq 1 ]; then CURRENT_TMP="$out_dir/dedup_input_$filename" echo "Removing duplicate read names..." dedupe_fastq \\ "$file" \\ "$CURRENT_TMP" input_for_filtlong="$CURRENT_TMP" else input_for_filtlong="$file" fi echo "Running Filtlong through Conda..." echo "$CONDA_EXE" run \\ --no-capture-output \\ -n "$ENV_NAME" \\ filtlong \\ ${filtlongParameterLines} \\ "$input_for_filtlong" > "$output_file" if [ -n "$CURRENT_TMP" ]; then rm -f "$CURRENT_TMP" CURRENT_TMP="" fi if [ ! -s "$output_file" ]; then echo echo "WARNING: Filtlong created an empty output file:" echo " $output_file" else input_size="$( du -h "$file" | awk '{print $1}' )" output_size="$( du -h "$output_file" | awk '{print $1}' )" echo echo "Output file:" echo " $output_file" echo echo "Input size: $input_size" echo "Output size: $output_size" fi done } processed_folder_count=0 if [ "$ITERATE_SUBFOLDERS" -eq 1 ]; then echo echo "Processing immediate subfolders of:" echo " $BASE_DIR" shopt -s nullglob subfolders=( "$BASE_DIR"/*/ ) shopt -u nullglob for folder in "\${subfolders[@]}"; do [ -d "$folder" ] || continue folder_clean="\${folder%/}" # Do not process the current Filtlong output folder. if [ "$folder_clean" = "$PARENT_OUT_DIR" ]; then continue fi process_folder "$folder_clean" processed_folder_count=$((processed_folder_count + 1)) done if [ "$processed_folder_count" -eq 0 ]; then echo echo "WARNING: No immediate subfolders were found." fi else process_folder "$BASE_DIR" fi echo echo "============================================================" echo "Filtlong filtering complete" echo echo "Minimum mean accuracy: ${minAccuracyText}%" echo "Approximate equivalent Q: Q${qDisplay}" echo echo "Parent output folder:" echo " $PARENT_OUT_DIR" echo "============================================================" echo echo "Press Enter to close..." read -r _

Filtlong controls

${folderPathInput} ${envInput} ${iterateSubfoldersInput} ${dedupeInput} ${minReadLengthInput} ${minAccuracyInput} ${qualityInfo} ${targetBasesInput}

Run on your Mac:
Copy the complete generated script and paste it directly into Terminal.

This version uses conda run. It does not call conda activate or execute Conda shell activation and deactivation hooks.

Turn off Iterate immediate subfolders when the FASTQ files are located directly inside the selected parent folder.

${copyBtn}

${status}

`; const scriptPanel = html`

Generated Mac Terminal script

${textarea}

`; const details = html`

▶ Filtlong filtering — macOS script

${controlsPanel} ${scriptPanel}

`; details.addEventListener("toggle", () => { details.querySelector("summary").textContent = details.open ? "▼ Filtlong filtering — macOS script" : "▶ Filtlong filtering — macOS script"; }); [ folderPathInput, envInput, iterateSubfoldersInput, dedupeInput, minReadLengthInput, minAccuracyInput, targetBasesInput ].forEach((element) => { element.addEventListener("input", generateCommand); }); copyBtn.addEventListener("click", async () => { try { await navigator.clipboard.writeText(textarea.value); status.textContent = "✅ Mac script copied to the clipboard."; } catch (error) { textarea.focus(); textarea.select(); const copied = document.execCommand("copy"); status.textContent = copied ? "✅ Mac script copied to the clipboard." : "❌ Copy failed. Select the script and copy it manually."; } }); generateCommand(); return details; } 36:T345d,viewof chopperScriptGenerator = { const fastqFolderInput = Inputs.text({ label: "📂 Path to folder containing FASTQ files (Mac-style)", placeholder: "/Users/YourName/Desktop/Nanopore_Results/Run1/Demux_Output", style: "width: 600px" }); const envInput = Inputs.text({ label: "🧪 Conda environment", value: "reads-assembly-core", style: "width: 320px" }); const filePatternInput = Inputs.text({ label: "🧬 FASTQ filename pattern", value: "*.fastq*", placeholder: "*.fastq*", style: "width: 420px" }); const recursiveInput = Inputs.toggle({ label: "🔍 Search subfolders recursively", value: true }); const recreateFoldersInput = Inputs.toggle({ label: "🔁 Recreate folder structure inside Chopper output", value: true }); const options = { quality: Inputs.range([0, 30], { label: "Min Q-score (-q)", step: 1, value: 10 }), minLength: Inputs.range([0, 10000], { label: "Min read length (-l)", step: 100, value: 300 }), maxLength: Inputs.range([0, 100000], { label: "Max read length (--maxlength)", step: 500, value: 50000 }), threads: Inputs.range([1, 64], { label: "Threads (-t)", step: 1, value: 4 }) }; const outputBox = html``; const copyButton = html``; function cleanMacPath(path) { let cleaned = String(path ?? "").trim(); if ( (cleaned.startsWith('"') && cleaned.endsWith('"')) || (cleaned.startsWith("'") && cleaned.endsWith("'")) ) { cleaned = cleaned.slice(1, -1); } // Convert paths copied from Terminal that contain escaped spaces. cleaned = cleaned.replace(/\\ /g, " "); return cleaned; } function shQuote(value) { return `'${String(value).replace(/'/g, `'\\''`)}'`; } function updateScript() { const fastqPath = cleanMacPath(fastqFolderInput.value); const envName = String(envInput.value ?? "").trim() || "reads-assembly-core"; const filePattern = String(filePatternInput.value ?? "").trim() || "*.fastq*"; const recursive = recursiveInput.value ? 1 : 0; const recreateFolders = recreateFoldersInput.value ? 1 : 0; const quality = Number(options.quality.value); const minLength = Number(options.minLength.value); const maxLength = Number(options.maxLength.value); const threads = Number(options.threads.value); const filteredFolder = `Chopper_Filtered_Q${quality}` + `_L${minLength}` + `_Max${maxLength}`; const script = `bash <<'CHOPPER_SCRIPT' #!/usr/bin/env bash # Do not enable "set -u" until after Conda is activated. # Some Conda macOS activation/deactivation hooks reference optional # backup variables that may not be defined. set -Eeo pipefail CURRENT_TMP="" pause_before_exit() { echo echo "Press Enter to close..." read -r _ /dev/null 2>&1; then command -v conda return 0 fi local possible_conda_locations=( "/opt/miniconda3/bin/conda" "/opt/anaconda3/bin/conda" "/usr/local/miniconda3/bin/conda" "/usr/local/anaconda3/bin/conda" "$HOME/miniconda3/bin/conda" "$HOME/anaconda3/bin/conda" "$HOME/miniforge3/bin/conda" "$HOME/mambaforge/bin/conda" ) local location for location in "\${possible_conda_locations[@]}"; do if [ -x "$location" ]; then printf '%s\\n' "$location" return 0 fi done return 1 } strip_fastq_extension() { local filename="$1" case "$filename" in *.fastq.gz) printf '%s\\n' "\${filename%.fastq.gz}" ;; *.fq.gz) printf '%s\\n' "\${filename%.fq.gz}" ;; *.fastq) printf '%s\\n' "\${filename%.fastq}" ;; *.fq) printf '%s\\n' "\${filename%.fq}" ;; *) printf '%s\\n' "$filename" ;; esac } echo echo "==============================================" echo "🧬 Chopper FASTQ filtering" echo "==============================================" echo INPUT_DIR="$(expand_user_path "$INPUT_DIR_RAW")" if [ "$INPUT_DIR" != "/" ]; then INPUT_DIR="\${INPUT_DIR%/}" fi if [ -z "$INPUT_DIR" ]; then echo "❌ No FASTQ folder was provided." pause_before_exit exit 1 fi if [ ! -d "$INPUT_DIR" ]; then echo "❌ Folder not found:" echo " $INPUT_DIR" pause_before_exit exit 1 fi echo "🧪 Locating Conda..." CONDA_EXE="$(find_conda_executable || true)" if [ -z "$CONDA_EXE" ]; then echo "❌ Conda could not be found." echo echo "Checked common locations including:" echo " /opt/miniconda3" echo " /opt/anaconda3" echo " $HOME/miniconda3" echo " $HOME/miniforge3" pause_before_exit exit 1 fi CONDA_BASE="$("$CONDA_EXE" info --base)" if [ ! -f "$CONDA_BASE/etc/profile.d/conda.sh" ]; then echo "❌ Conda initialization file was not found:" echo " $CONDA_BASE/etc/profile.d/conda.sh" pause_before_exit exit 1 fi echo "🧪 Conda base:" echo " $CONDA_BASE" # Keep nounset disabled while loading Conda. set +u # shellcheck source=/dev/null source "$CONDA_BASE/etc/profile.d/conda.sh" echo echo "🧪 Activating Conda environment: $ENV_NAME" if ! conda activate "$ENV_NAME"; then echo echo "❌ Could not activate Conda environment: $ENV_NAME" echo echo "Available Conda environments:" conda env list || true pause_before_exit exit 1 fi # Conda activation has finished. Strict undefined-variable checking # can now be safely enabled for the remainder of this script. set -u echo "✅ Conda environment activated:" echo " $CONDA_DEFAULT_ENV" if ! command -v chopper >/dev/null 2>&1; then echo echo "❌ Chopper was not found in Conda environment: $ENV_NAME" echo echo "Install Chopper with:" echo " conda install -n $ENV_NAME -c bioconda chopper" pause_before_exit exit 1 fi OUTPUT_ROOT="$INPUT_DIR/$OUTPUT_FOLDER_NAME" mkdir -p "$OUTPUT_ROOT" echo echo "✅ Chopper found:" echo " $(command -v chopper)" echo echo "🧬 Chopper version:" chopper --version || true echo echo "📂 Input folder:" echo " $INPUT_DIR" echo echo "📂 Output folder:" echo " $OUTPUT_ROOT" echo echo "🔎 FASTQ pattern: $FILE_PATTERN" echo "🔍 Recursive search: $RECURSIVE" echo "🔁 Recreate folders: $RECREATE_FOLDERS" echo echo "⚙️ Chopper settings:" echo " Minimum Q-score: $MIN_QUALITY" echo " Minimum length: $MIN_LENGTH bp" echo " Maximum length: $MAX_LENGTH bp" echo " Threads: $THREADS" echo echo "🔍 Searching for FASTQ files..." files=() if [ "$RECURSIVE" -eq 1 ]; then while IFS= read -r -d '' file; do files[\${#files[@]}]="$file" done < <( find "$INPUT_DIR" \\ -type f \\ -iname "$FILE_PATTERN" \\ ! -path "$OUTPUT_ROOT/*" \\ ! -path "*/Chopper_Filtered_*/*" \\ ! -path "*/nanocomp_output/*" \\ -print0 ) else while IFS= read -r -d '' file; do files[\${#files[@]}]="$file" done < <( find "$INPUT_DIR" \\ -maxdepth 1 \\ -type f \\ -iname "$FILE_PATTERN" \\ -print0 ) fi file_count=\${#files[@]} echo "✅ Found $file_count matching FASTQ file(s)." if [ "$file_count" -eq 0 ]; then echo echo "❌ No matching FASTQ files were found." echo echo "Possible solutions:" echo " • Use the pattern *.fastq*" echo " • Enable recursive searching" echo " • Confirm the selected folder" pause_before_exit exit 1 fi processed_count=0 empty_count=0 for file in "\${files[@]}"; do base_name="$(basename "$file")" stem="$(strip_fastq_extension "$base_name")" relative_path="\${file#"$INPUT_DIR"/}" if [ "$RECREATE_FOLDERS" -eq 1 ]; then relative_directory="$(dirname "$relative_path")" if [ "$relative_directory" = "." ]; then output_directory="$OUTPUT_ROOT" else output_directory="$OUTPUT_ROOT/$relative_directory" fi output_name="filtered_$stem.fastq" else output_directory="$OUTPUT_ROOT" # Include the relative directory in flattened filenames so that # identical FASTQ filenames from different folders are not overwritten. flattened_name="\${relative_path//\\//__}" flattened_stem="$(strip_fastq_extension "$flattened_name")" output_name="filtered_$flattened_stem.fastq" fi mkdir -p "$output_directory" output_file="$output_directory/$output_name" CURRENT_TMP="$output_file.tmp.$$" rm -f "$CURRENT_TMP" echo echo "----------------------------------------------" echo "🔍 Processing:" echo " $file" echo echo "➡ Output:" echo " $output_file" if [[ "$file" == *.gz ]]; then gzip -cd -- "$file" | chopper \\ -q "$MIN_QUALITY" \\ -l "$MIN_LENGTH" \\ --maxlength "$MAX_LENGTH" \\ -t "$THREADS" \\ > "$CURRENT_TMP" else chopper \\ -q "$MIN_QUALITY" \\ -l "$MIN_LENGTH" \\ --maxlength "$MAX_LENGTH" \\ -t "$THREADS" \\ < "$file" \\ > "$CURRENT_TMP" fi mv -f "$CURRENT_TMP" "$output_file" CURRENT_TMP="" processed_count=$((processed_count + 1)) if [ ! -s "$output_file" ]; then empty_count=$((empty_count + 1)) echo "⚠️ No reads passed the filters." echo " An empty FASTQ file was created." else output_size="$(du -h "$output_file" | cut -f1)" echo "✅ Finished." echo " Output size: $output_size" fi done echo echo "==============================================" echo "✅ Chopper filtering complete" echo "==============================================" echo echo "Processed files: $processed_count" echo "Empty outputs: $empty_count" echo echo "📁 Filtered FASTQ files were saved in:" echo " $OUTPUT_ROOT" pause_before_exit CHOPPER_SCRIPT `; outputBox.value = script; } fastqFolderInput.addEventListener("input", updateScript); envInput.addEventListener("input", updateScript); filePatternInput.addEventListener("input", updateScript); recursiveInput.addEventListener("input", updateScript); recreateFoldersInput.addEventListener("input", updateScript); options.quality.addEventListener("input", updateScript); options.minLength.addEventListener("input", updateScript); options.maxLength.addEventListener("input", updateScript); options.threads.addEventListener("input", updateScript); copyButton.onclick = async () => { try { await navigator.clipboard.writeText(outputBox.value); copyButton.textContent = "✅ Copied"; setTimeout(() => { copyButton.textContent = "📋 Copy Mac Script"; }, 2000); } catch (error) { outputBox.focus(); outputBox.select(); document.execCommand("copy"); copyButton.textContent = "✅ Copied"; setTimeout(() => { copyButton.textContent = "📋 Copy Mac Script"; }, 2000); } }; updateScript(); return html`

⬇ Chopper filtering script generator — macOS

${fastqFolderInput} ${envInput} ${filePatternInput} ${recursiveInput} ${recreateFoldersInput} ${options.quality} ${options.minLength} ${options.maxLength} ${options.threads} ${copyButton}

${outputBox}

`; }37:T4471,viewof flyeGithubInstaller = { ///////////////////////////////////////////////////////////////////////////// // CONTROLS ///////////////////////////////////////////////////////////////////////////// const envInput = Inputs.text({ label: "🧪 Conda environment name", value: "reads-assembly-core", style: "width:100%;" }); const refInput = Inputs.text({ label: "🌿 GitHub branch, tag, or commit", value: "flye", placeholder: "flye", style: "width:100%;" }); const reinstallInput = Inputs.toggle({ label: "♻️ Replace an existing Flye installation", value: true }); const testInput = Inputs.toggle({ label: "🧪 Run Flye's toy-data test after installation", value: true }); ///////////////////////////////////////////////////////////////////////////// // OUTPUT ELEMENTS ///////////////////////////////////////////////////////////////////////////// const textarea = html``; const copyBtn = html``; const status = html``; const arrow = html` ▶ `; ///////////////////////////////////////////////////////////////////////////// // HELPERS ///////////////////////////////////////////////////////////////////////////// function shQuote(value) { return "'" + String(value).replace(/'/g, "'\"'\"'") + "'"; } ///////////////////////////////////////////////////////////////////////////// // SCRIPT GENERATOR ///////////////////////////////////////////////////////////////////////////// function generateScript() { const envName = String(envInput.value || "").trim() || "reads-assembly-core"; const flyeRef = String(refInput.value || "").trim() || "flye"; const reinstall = reinstallInput.value ? "1" : "0"; const runTest = testInput.value ? "1" : "0"; const innerScript = `#!/usr/bin/env bash set -Eeuo pipefail export PATH="/opt/homebrew/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:\${PATH:-}" ENV_NAME=${shQuote(envName)} FLYE_REF=${shQuote(flyeRef)} REINSTALL_FLYE=${shQuote(reinstall)} RUN_TOY_TEST=${shQuote(runTest)} REPO_URL="https://github.com/mikolmogorov/Flye.git" WORKDIR="" cleanup() { if [ -n "\${WORKDIR}" ] && [ -d "\${WORKDIR}" ]; then rm -rf "\${WORKDIR}" fi } pause_for_user() { echo if [ -r /dev/tty ]; then read -r -p "Press Enter to close..." _ /dev/null 2>&1; then command -v conda return 0 fi for candidate in \\ "/opt/miniconda3/bin/conda" \\ "/opt/miniforge3/bin/conda" \\ "/opt/anaconda3/bin/conda" \\ "/usr/local/miniconda3/bin/conda" \\ "/usr/local/miniforge3/bin/conda" \\ "/usr/local/anaconda3/bin/conda" \\ "\${HOME}/miniconda3/bin/conda" \\ "\${HOME}/miniforge3/bin/conda" \\ "\${HOME}/anaconda3/bin/conda" \\ "\${HOME}/mambaforge/bin/conda" \\ "/opt/homebrew/Caskroom/miniconda/base/bin/conda" do if [ -x "\${candidate}" ]; then printf '%s\\n' "\${candidate}" return 0 fi done return 1 } echo echo "============================================================" echo " Flye GitHub installer for macOS" echo "============================================================" echo echo "Conda environment: \${ENV_NAME}" echo "GitHub ref: \${FLYE_REF}" echo if [ "$(uname -s)" != "Darwin" ]; then echo "❌ This installer is intended for macOS." echo "Detected operating system: $(uname -s)" pause_for_user exit 1 fi if [[ ! "\${ENV_NAME}" =~ ^[A-Za-z0-9._-]+$ ]]; then echo "❌ Invalid Conda environment name:" echo "\${ENV_NAME}" echo echo "Use only letters, numbers, periods, underscores, and hyphens." pause_for_user exit 1 fi if ! xcode-select -p >/dev/null 2>&1; then echo "❌ Apple Command Line Tools are not installed." echo echo "Run:" echo echo " xcode-select --install" echo echo "Complete the Apple installer and then run this script again." pause_for_user exit 1 fi echo "✅ Apple Command Line Tools found:" echo "$(xcode-select -p)" echo CONDA_EXE="$( find_conda || true )" if [ -z "\${CONDA_EXE}" ]; then echo "❌ Conda was not found." echo echo "The script checked common Miniconda, Miniforge," echo "Mambaforge, and Anaconda installation locations." pause_for_user exit 1 fi CONDA_BASE="$( "\${CONDA_EXE}" info --base )" echo "✅ Conda executable:" echo "\${CONDA_EXE}" echo echo "Conda base:" echo "\${CONDA_BASE}" echo ############################################################################## # DETERMINE WHETHER THE ENVIRONMENT EXISTS ############################################################################## ENV_PREFIX="$( "\${CONDA_EXE}" env list --json | "\${CONDA_BASE}/bin/python" -c ' import json import os import sys environment_name = sys.argv[1] for environment_path in json.load(sys.stdin).get("envs", []): if os.path.basename(environment_path.rstrip(os.sep)) == environment_name: print(environment_path) break ' "\${ENV_NAME}" )" ############################################################################## # CREATE OR UPDATE THE ENVIRONMENT # # The environment is not activated. Using conda with -n avoids the macOS # compiler activation/deactivation hooks that caused the unbound-variable # error. ############################################################################## if [ -z "\${ENV_PREFIX}" ]; then echo "📦 Creating Conda environment:" echo "\${ENV_NAME}" echo "\${CONDA_EXE}" create \\ --yes \\ --name "\${ENV_NAME}" \\ --channel conda-forge \\ python=3.11 \\ pip \\ setuptools \\ wheel \\ make \\ zlib \\ git else echo "✅ Conda environment already exists:" echo "\${ENV_PREFIX}" echo echo "📦 Installing or updating build dependencies" echo "\${CONDA_EXE}" install \\ --yes \\ --name "\${ENV_NAME}" \\ --channel conda-forge \\ python=3.11 \\ pip \\ setuptools \\ wheel \\ make \\ zlib \\ git fi ############################################################################## # GET THE EXACT ENVIRONMENT PREFIX ############################################################################## ENV_PREFIX="$( "\${CONDA_EXE}" run \\ --name "\${ENV_NAME}" \\ python -c 'import sys; print(sys.prefix)' )" ENV_PYTHON="\${ENV_PREFIX}/bin/python" ENV_FLYE="\${ENV_PREFIX}/bin/flye" ENV_GIT="\${ENV_PREFIX}/bin/git" echo echo "✅ Target Conda environment:" echo "\${ENV_PREFIX}" echo echo "Environment Python:" echo "\${ENV_PYTHON}" echo if [ ! -x "\${ENV_PYTHON}" ]; then echo "❌ Python was not found inside the target environment:" echo "\${ENV_PYTHON}" pause_for_user exit 1 fi if [ ! -x "\${ENV_GIT}" ]; then echo "❌ Git was not found inside the target environment:" echo "\${ENV_GIT}" pause_for_user exit 1 fi HOST_ARCH="$(uname -m)" PYTHON_ARCH="$( "\${ENV_PYTHON}" -c ' import platform print(platform.machine()) ' )" echo "Mac architecture: \${HOST_ARCH}" echo "Python architecture: \${PYTHON_ARCH}" echo if [ "\${HOST_ARCH}" != "\${PYTHON_ARCH}" ]; then echo "⚠️ The Terminal and Conda Python architectures differ." echo "The build may run under Rosetta." echo "Native matching architectures are recommended." echo fi ############################################################################## # UPDATE PYTHON BUILD TOOLS IN THE EXACT TARGET ENVIRONMENT ############################################################################## echo "📦 Updating Python build tools in:" echo "\${ENV_PREFIX}" echo "\${ENV_PYTHON}" -m pip install \\ --upgrade \\ pip \\ setuptools \\ wheel ############################################################################## # DOWNLOAD FLYE ############################################################################## WORKDIR="$( mktemp -d "\${TMPDIR:-/tmp}/flye-github.XXXXXX" )" SOURCE_DIR="\${WORKDIR}/Flye" echo echo "⬇️ Cloning Flye from GitHub" echo "Repository: \${REPO_URL}" echo "Ref: \${FLYE_REF}" echo if ! "\${ENV_GIT}" clone \\ --depth 1 \\ --branch "\${FLYE_REF}" \\ "\${REPO_URL}" \\ "\${SOURCE_DIR}" then echo echo "The requested ref could not be cloned as a branch or tag." echo "Trying a complete clone followed by checkout." echo rm -rf "\${SOURCE_DIR}" "\${ENV_GIT}" clone \\ "\${REPO_URL}" \\ "\${SOURCE_DIR}" "\${ENV_GIT}" -C "\${SOURCE_DIR}" checkout "\${FLYE_REF}" fi GIT_COMMIT="$( "\${ENV_GIT}" -C "\${SOURCE_DIR}" rev-parse --short HEAD )" echo echo "✅ Checked out Git commit:" echo "\${GIT_COMMIT}" echo ############################################################################## # BUILD SETTINGS ############################################################################## SDKROOT="$( xcrun --sdk macosx --show-sdk-path )" export SDKROOT export PATH="\${ENV_PREFIX}/bin:\${PATH}" export CPPFLAGS="-I\${ENV_PREFIX}/include \${CPPFLAGS:-}" export LDFLAGS="\\ -Wl,-rpath,\${ENV_PREFIX}/lib \\ -L\${ENV_PREFIX}/lib \\ \${LDFLAGS:-}" echo "SDK root:" echo "\${SDKROOT}" echo ############################################################################## # REMOVE AN EXISTING INSTALLATION WHEN REQUESTED ############################################################################## if [ "\${REINSTALL_FLYE}" = "1" ]; then echo "♻️ Removing an existing Flye Python package, if present" echo "\${ENV_PYTHON}" -m pip uninstall \\ --yes \\ flye || true fi ############################################################################## # INSTALL FLYE USING THE TARGET ENVIRONMENT'S PYTHON ############################################################################## echo echo "🔨 Compiling and installing Flye" echo echo "Python used for installation:" echo "\${ENV_PYTHON}" echo PIP_INSTALL_ARGS=( --no-build-isolation --no-cache-dir ) if [ "\${REINSTALL_FLYE}" = "1" ]; then PIP_INSTALL_ARGS+=( --force-reinstall ) fi "\${ENV_PYTHON}" -m pip install \\ "\${PIP_INSTALL_ARGS[@]}" \\ "\${SOURCE_DIR}" ############################################################################## # VERIFY THE INSTALLATION ############################################################################## echo echo "🔎 Verifying Flye installation" echo if [ ! -x "\${ENV_FLYE}" ]; then echo "❌ Flye was not created at the expected location:" echo "\${ENV_FLYE}" echo echo "Flye package information:" "\${ENV_PYTHON}" -m pip show flye || true echo echo "Matching files in the environment bin folder:" find "\${ENV_PREFIX}/bin" \\ -maxdepth 1 \\ -iname "*flye*" \\ -print || true pause_for_user exit 1 fi echo "✅ Flye executable:" echo "\${ENV_FLYE}" echo "\${ENV_FLYE}" --version echo echo "Flye Python package:" "\${ENV_PYTHON}" -m pip show flye echo ############################################################################## # OPTIONAL TEST ############################################################################## if [ "\${RUN_TOY_TEST}" = "1" ]; then echo "🧪 Running Flye's included toy-data test" echo ( cd "\${SOURCE_DIR}" "\${ENV_PYTHON}" flye/tests/test_toy.py ) fi ############################################################################## # FINAL REPORT ############################################################################## echo echo "============================================================" echo " ✅ Flye was installed successfully" echo "============================================================" echo echo "Conda environment:" echo "\${ENV_NAME}" echo echo "Environment prefix:" echo "\${ENV_PREFIX}" echo echo "Flye executable:" echo "\${ENV_FLYE}" echo echo "Git commit:" echo "\${GIT_COMMIT}" echo echo "To verify Flye without activating the environment, run:" echo echo " \${CONDA_EXE} run -n \${ENV_NAME} flye --version" echo echo "To activate the environment manually, run:" echo echo " source \${CONDA_BASE}/etc/profile.d/conda.sh" echo " conda activate \${ENV_NAME}" echo " flye --version" echo pause_for_user`; textarea.value = `bash <<'FLYE_GITHUB_INSTALLER'\n` + innerScript + `\nFLYE_GITHUB_INSTALLER`; status.textContent = "Installer code updated"; } ///////////////////////////////////////////////////////////////////////////// // EVENTS ///////////////////////////////////////////////////////////////////////////// for (const control of [envInput, refInput, reinstallInput, testInput]) { control.addEventListener("input", generateScript); } copyBtn.addEventListener("click", async () => { try { await navigator.clipboard.writeText(textarea.value); copyBtn.textContent = "✅ Copied"; status.textContent = "Paste the copied code into macOS Terminal"; } catch (error) { textarea.focus(); textarea.select(); document.execCommand("copy"); copyBtn.textContent = "✅ Copied"; status.textContent = "Paste the copied code into macOS Terminal"; } setTimeout(() => { copyBtn.textContent = "📋 Copy Mac installer"; }, 1800); }); generateScript(); ///////////////////////////////////////////////////////////////////////////// // COLLAPSIBLE LAYOUT ///////////////////////////////////////////////////////////////////////////// const controlsPanel = html`

${envInput} ${refInput} ${reinstallInput} ${testInput}

Installation method
Flye is installed using the Python executable located directly inside the selected Conda environment. The script does not use conda activate, avoiding macOS Conda compiler-hook errors.

Expected Flye location
/opt/miniconda3/envs/reads-assembly-core/bin/flye

`; const outputPanel = html`

${textarea}

${copyBtn} ${status}

`; const installerWindow = html`

${arrow} 🧬 Flye GitHub Installer for macOS

${controlsPanel} ${outputPanel}

Run this installer again, then verify Flye using:


          /opt/miniconda3/bin/conda run -n reads-assembly-core
          flye --version

`; installerWindow.addEventListener("toggle", () => { arrow.textContent = installerWindow.open ? "▼" : "▶"; }); return installerWindow; }38:T4c8e,viewof flyeScriptGenerator = { ///////////////////////////////////////////////////////////////////////////// // INPUT CONTROLS ///////////////////////////////////////////////////////////////////////////// const inputPath = Inputs.text({ label: "📂 Path to folder containing FASTQ files (macOS-style)", placeholder: "/Users/YourName/Desktop/Nanopore_Results/Run1/Demux_Output", style: "width:100%;" }); const envInput = Inputs.text({ label: "🧪 Conda environment", value: "reads-assembly-core", style: "width:100%;" }); const readTypeInput = Inputs.select(["--nano-hq", "--nano-raw"], { label: "🧬 Flye read type", value: "--nano-hq", style: "width:100%;" }); const genomeSizeInput = Inputs.text({ label: "🧫 Expected genome size", value: "50k", placeholder: "50k", style: "width:100%;" }); const flyeIterationsInput = Inputs.number({ label: "🔁 Flye polishing iterations", value: 1, min: 0, max: 10, step: 1, style: "width:100%;" }); const asmCoverageInput = Inputs.number({ label: "📉 Flye asm coverage (0 = off)", value: 0, min: 0, step: 1, style: "width:100%;" }); const threads = Inputs.range([1, 32], { label: "🧵 Threads", value: 4, step: 1 }); const minOverlap = Inputs.number({ label: "🔗 Flye min overlap (0 = auto)", value: 0, min: 0, step: 100, style: "width:100%;" }); const recursiveInput = Inputs.toggle({ label: "🔍 Search subfolders", value: true }); ///////////////////////////////////////////////////////////////////////////// // OUTPUT ELEMENTS ///////////////////////////////////////////////////////////////////////////// const textarea = html``; const copyBtn = html``; const status = html``; const arrow = html` ▶ `; ///////////////////////////////////////////////////////////////////////////// // HELPERS ///////////////////////////////////////////////////////////////////////////// function normalizeMacPath(value) { let path = String(value || "").trim(); if ( (path.startsWith('"') && path.endsWith('"')) || (path.startsWith("'") && path.endsWith("'")) ) { path = path.slice(1, -1); } path = path.replace(/\\ /g, " "); if (path.length > 1) { path = path.replace(/\/+$/, ""); } return path; } function shQuote(value) { return "'" + String(value).replace(/'/g, "'\"'\"'") + "'"; } function generateScript() { const basePath = normalizeMacPath(inputPath.value); if (!basePath) { textarea.value = "# Enter the macOS path to the folder containing the FASTQ files."; status.textContent = "Enter a FASTQ folder path"; return; } const envName = String(envInput.value || "").trim() || "reads-assembly-core"; const readType = String(readTypeInput.value || "").trim() || "--nano-hq"; const genomeSize = String(genomeSizeInput.value || "").trim() || "50k"; const flyeIterations = Number.isFinite(Number(flyeIterationsInput.value)) ? Math.max(0, Math.floor(Number(flyeIterationsInput.value))) : 1; const asmCoverage = Number.isFinite(Number(asmCoverageInput.value)) ? Math.max(0, Math.floor(Number(asmCoverageInput.value))) : 0; const threadCount = Number.isFinite(Number(threads.value)) ? Math.max(1, Math.floor(Number(threads.value))) : 4; const minOverlapValue = Number.isFinite(Number(minOverlap.value)) ? Math.max(0, Math.floor(Number(minOverlap.value))) : 0; const recursive = recursiveInput.value ? 1 : 0; const innerScript = `#!/usr/bin/env bash set -Eeuo pipefail export PATH="/opt/homebrew/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:\${PATH:-}" BASE_DIR=${shQuote(basePath)} CONDA_ENV=${shQuote(envName)} FLYE_READ_TYPE=${shQuote(readType)} GENOME_SIZE=${shQuote(genomeSize)} FLYE_ITERATIONS=${flyeIterations} ASM_COVERAGE=${asmCoverage} THREADS=${threadCount} MIN_OVERLAP=${minOverlapValue} RECURSIVE=${recursive} ASSEMBLIES_DIR="$BASE_DIR/assemblies" success_count=0 failure_count=0 found_count=0 pause_for_user() { echo if [ -r /dev/tty ]; then read -r -p "Press Enter to close..." _ /dev/null 2>&1; then conda_base="$( conda info --base 2>/dev/null || true )" if [ -n "$conda_base" ] && [ -f "$conda_base/etc/profile.d/conda.sh" ]; then printf '%s\\n' "$conda_base/etc/profile.d/conda.sh" return 0 fi fi for candidate in \\ "/opt/miniconda3/etc/profile.d/conda.sh" \\ "/opt/miniforge3/etc/profile.d/conda.sh" \\ "/opt/anaconda3/etc/profile.d/conda.sh" \\ "/usr/local/miniconda3/etc/profile.d/conda.sh" \\ "/usr/local/miniforge3/etc/profile.d/conda.sh" \\ "/usr/local/anaconda3/etc/profile.d/conda.sh" \\ "$HOME/miniconda3/etc/profile.d/conda.sh" \\ "$HOME/miniforge3/etc/profile.d/conda.sh" \\ "$HOME/anaconda3/etc/profile.d/conda.sh" \\ "$HOME/mambaforge/etc/profile.d/conda.sh" \\ "$HOME/miniconda/etc/profile.d/conda.sh" do if [ -f "$candidate" ]; then printf '%s\\n' "$candidate" return 0 fi done return 1 } sanitize_sample_name() { local original="$1" local cleaned="" cleaned="$( printf '%s' "$original" | tr ' /:()[]{}' '__________' | tr -cd 'A-Za-z0-9._-' )" while [[ "$cleaned" == *"__"* ]]; do cleaned="\${cleaned//__/_}" done cleaned="\${cleaned#_}" cleaned="\${cleaned%_}" if [ -z "$cleaned" ]; then cleaned="sample" fi printf '%s\\n' "$cleaned" } write_fasta_info() { local fasta_file="$1" local output_file="$2" local stage_name="$3" python - "$fasta_file" "$output_file" "$stage_name" <<'PYTHON_FASTA_INFO' import sys from pathlib import Path fasta_path = Path(sys.argv[1]) output_path = Path(sys.argv[2]) stage = sys.argv[3] sequences = [] current = [] with fasta_path.open( "r", encoding="utf-8", errors="replace" ) as handle: for raw_line in handle: line = raw_line.strip() if not line: continue if line.startswith(">"): if current: sequences.append("".join(current)) current = [] else: current.append(line) if current: sequences.append("".join(current)) lengths = sorted( (len(sequence) for sequence in sequences), reverse=True ) sequence_count = len(lengths) total_bases = sum(lengths) longest_sequence = lengths[0] if lengths else 0 shortest_sequence = lengths[-1] if lengths else 0 n50 = 0 if total_bases > 0: halfway = total_bases / 2 cumulative = 0 for length in lengths: cumulative += length if cumulative >= halfway: n50 = length break gc_bases = 0 atgc_bases = 0 for sequence in sequences: upper = sequence.upper() gc_bases += upper.count("G") gc_bases += upper.count("C") atgc_bases += upper.count("A") atgc_bases += upper.count("T") atgc_bases += upper.count("G") atgc_bases += upper.count("C") gc_percent = ( 100.0 * gc_bases / atgc_bases if atgc_bases else 0.0 ) output_path.parent.mkdir( parents=True, exist_ok=True ) with output_path.open( "w", encoding="utf-8" ) as output: output.write( "Stage\\tFASTA_File\\tSequence_Count\\t" "Total_Bases\\tLongest_Sequence\\t" "Shortest_Sequence\\tN50\\tGC_Percent\\n" ) output.write( f"{stage}\\t" f"{fasta_path.name}\\t" f"{sequence_count}\\t" f"{total_bases}\\t" f"{longest_sequence}\\t" f"{shortest_sequence}\\t" f"{n50}\\t" f"{gc_percent:.2f}\\n" ) PYTHON_FASTA_INFO } echo echo "==========================================" echo " Flye assembly pipeline" echo "==========================================" echo if [ "$(uname -s)" != "Darwin" ]; then echo "❌ This script is intended for macOS." echo "Detected operating system: $(uname -s)" pause_for_user exit 1 fi if [ ! -d "$BASE_DIR" ]; then echo "❌ FASTQ folder not found:" echo "$BASE_DIR" pause_for_user exit 1 fi if [[ ! "$CONDA_ENV" =~ ^[A-Za-z0-9._-]+$ ]]; then echo "❌ Invalid Conda environment name:" echo "$CONDA_ENV" echo echo "Use only letters, numbers, periods, underscores, and hyphens." pause_for_user exit 1 fi CONDA_SCRIPT="$( find_conda_script || true )" if [ -z "$CONDA_SCRIPT" ]; then echo "❌ Conda initialization file could not be found." echo echo "The script checked common Miniconda, Miniforge," echo "Mambaforge, and Anaconda installation locations." pause_for_user exit 1 fi echo "Conda initialization:" echo "$CONDA_SCRIPT" echo ############################################################################## # CONDA NOUNSET FIX # # Conda's macOS compiler activation and deactivation scripts may reference # backup variables that are not defined. Temporarily turn off Bash nounset # checking while Conda is sourced and the environment is activated. ############################################################################## NOUNSET_WAS_ENABLED=0 case "$-" in *u*) NOUNSET_WAS_ENABLED=1 set +u ;; esac # shellcheck disable=SC1090 source "$CONDA_SCRIPT" if ! conda activate "$CONDA_ENV"; then if [ "$NOUNSET_WAS_ENABLED" -eq 1 ]; then set -u fi echo echo "❌ Could not activate Conda environment:" echo "$CONDA_ENV" echo echo "Available Conda environments:" conda env list || true pause_for_user exit 1 fi if [ "$NOUNSET_WAS_ENABLED" -eq 1 ]; then set -u fi unset NOUNSET_WAS_ENABLED echo "✅ Activated Conda environment: $CONDA_ENV" echo "Conda prefix: \${CONDA_PREFIX:-Not available}" echo missing_tools="" for tool in flye python do if ! command -v "$tool" >/dev/null 2>&1; then missing_tools="$missing_tools $tool" fi done if [ -n "$missing_tools" ]; then echo "❌ Required programs are missing from $CONDA_ENV:" echo "$missing_tools" echo echo "Install Flye in the selected environment before running this pipeline." pause_for_user exit 1 fi echo "Flye executable:" command -v flye echo echo "Flye version:" flye --version || true echo echo "Pipeline settings:" echo "FASTQ folder: $BASE_DIR" echo "Output folder: $ASSEMBLIES_DIR" echo "Conda environment: $CONDA_ENV" echo "Read type: $FLYE_READ_TYPE" echo "Genome size: $GENOME_SIZE" echo "Flye iterations: $FLYE_ITERATIONS" echo "Assembly coverage: $ASM_COVERAGE" echo "Threads: $THREADS" echo "Minimum overlap: $MIN_OVERLAP" echo "Search subfolders: $RECURSIVE" echo mkdir -p "$ASSEMBLIES_DIR" while IFS= read -r -d '' file do file_parent="$(dirname "$file")" if [ "$RECURSIVE" -ne 1 ] && [ "$file_parent" != "$BASE_DIR" ]; then continue fi found_count=$((found_count + 1)) file_name="$(basename "$file")" parent_name="$(basename "$file_parent")" if [ "$file_parent" = "$BASE_DIR" ]; then sample_raw="$file_name" case "$sample_raw" in *.fastq.gz) sample_raw="\${sample_raw%.fastq.gz}" ;; *.fq.gz) sample_raw="\${sample_raw%.fq.gz}" ;; *.fastq) sample_raw="\${sample_raw%.fastq}" ;; *.fq) sample_raw="\${sample_raw%.fq}" ;; esac else sample_raw="$parent_name" fi sample="$( sanitize_sample_name "$sample_raw" )" sample_dir="$ASSEMBLIES_DIR/$sample" echo echo "==========================================" echo " Processing sample: $sample" echo "==========================================" echo echo "FASTQ file:" echo "$file" echo echo "Flye output:" echo "$sample_dir" echo if [ -d "$sample_dir" ]; then echo "♻️ Removing existing output folder:" echo "$sample_dir" rm -rf "$sample_dir" fi mkdir -p "$sample_dir" flye_args=( "$FLYE_READ_TYPE" "$file" "--out-dir" "$sample_dir" "--threads" "$THREADS" "--genome-size" "$GENOME_SIZE" "--iterations" "$FLYE_ITERATIONS" ) if [ "$MIN_OVERLAP" -gt 0 ]; then flye_args+=( "--min-overlap" "$MIN_OVERLAP" ) fi if [ "$ASM_COVERAGE" -gt 0 ]; then flye_args+=( "--asm-coverage" "$ASM_COVERAGE" ) fi echo "Running Flye:" printf ' %q' flye "\${flye_args[@]}" echo echo if ! flye "\${flye_args[@]}"; then echo echo "❌ Flye failed for: $sample" failure_count=$((failure_count + 1)) continue fi assembly="$sample_dir/assembly.fasta" final="$sample_dir/\${sample}_flye_assembly.fasta" if [ ! -s "$assembly" ]; then echo echo "❌ Flye did not create a non-empty assembly.fasta:" echo "$assembly" failure_count=$((failure_count + 1)) continue fi cp -f "$assembly" "$final" if [ -f "$sample_dir/assembly_info.txt" ]; then cp -f \\ "$sample_dir/assembly_info.txt" \\ "$sample_dir/\${sample}_flye_assembly_info.txt" fi fasta_info="$sample_dir/\${sample}_flye_fasta_info.tsv" write_fasta_info "$final" "$fasta_info" "flye" echo echo "📄 Flye FASTA summary:" cat "$fasta_info" echo echo "✅ Finished: $sample" echo echo "Sample-named assembly:" echo "$final" success_count=$((success_count + 1)) done < <( find "$BASE_DIR" \\ -path "$ASSEMBLIES_DIR" -prune -o \\ -type f \\ \$ \\ -iname "*.fastq" -o \\ -iname "*.fq" -o \\ -iname "*.fastq.gz" -o \\ -iname "*.fq.gz" \\ \$ \\ -print0 ) if [ "$found_count" -eq 0 ]; then echo echo "❌ No FASTQ files were found." echo echo "Search folder:" echo "$BASE_DIR" failure_count=$((failure_count + 1)) fi echo echo "==========================================" echo " Flye assembly pipeline complete" echo "==========================================" echo echo "FASTQ files found: $found_count" echo "Successful assemblies: $success_count" echo "Failed assemblies: $failure_count" echo echo "Assembly output folder:" echo "$ASSEMBLIES_DIR" pause_for_user`; textarea.value = `bash <<'FLYE_MAC_SCRIPT'\n` + innerScript + `\nFLYE_MAC_SCRIPT`; status.textContent = "Mac script updated"; } ///////////////////////////////////////////////////////////////////////////// // COPY BUTTON ///////////////////////////////////////////////////////////////////////////// copyBtn.addEventListener("click", async () => { try { await navigator.clipboard.writeText(textarea.value); copyBtn.textContent = "✅ Copied"; status.textContent = "Paste the copied code into macOS Terminal"; } catch (error) { textarea.focus(); textarea.select(); document.execCommand("copy"); copyBtn.textContent = "✅ Copied"; status.textContent = "Paste the copied code into macOS Terminal"; } setTimeout(() => { copyBtn.textContent = "📋 Copy Mac Script code"; }, 1800); }); ///////////////////////////////////////////////////////////////////////////// // UPDATE SCRIPT WHEN CONTROLS CHANGE ///////////////////////////////////////////////////////////////////////////// for (const control of [ inputPath, envInput, readTypeInput, genomeSizeInput, flyeIterationsInput, asmCoverageInput, threads, minOverlap, recursiveInput ]) { control.addEventListener("input", generateScript); } generateScript(); ///////////////////////////////////////////////////////////////////////////// // COLLAPSIBLE WINDOW ///////////////////////////////////////////////////////////////////////////// const controlsPanel = html`

${inputPath} ${envInput} ${readTypeInput} ${genomeSizeInput} ${flyeIterationsInput} ${asmCoverageInput} ${threads} ${minOverlap} ${recursiveInput}

Output structure
Each FASTQ sample receives its own folder inside assemblies. The final FASTA is copied to a sample-named file, and a TSV summary is generated.

`; const outputPanel = html`

${textarea}

${copyBtn} ${status}

`; const panel = html`

⬇ Flye assembly macOS script

${controlsPanel} ${outputPanel}

Copy the entire generated block and paste it into the macOS Terminal. The script activates the selected Conda environment before running Flye.

`; panel.addEventListener("toggle", () => { arrow.textContent = panel.open ? "▼" : "▶"; }); return panel; }39:T75bd,viewof combineAssemblyMacScript = { const fullWidthInputStyle = "width:100%; max-width:100%; box-sizing:border-box;"; const inputPath = Inputs.text({ label: "📂 Folder containing assembly subfolders (Mac path)", placeholder: "/Users/yourname/Desktop/Nanopore_Results/Run1/Sample1/assemblies", style: fullWidthInputStyle }); const envInput = Inputs.text({ label: "🧪 Conda environment", value: "reads-assembly-core", style: fullWidthInputStyle }); const contigSelection = Inputs.checkbox(["Keep all contigs"], { label: "Contig selection", value: ["Keep all contigs"] }); const barcodeMapPath = Inputs.text({ label: "🧬 Optional barcode-to-phage Excel file (Mac path)", placeholder: "/Users/yourname/Desktop/barcode_to_phage.xlsx", value: "", style: fullWidthInputStyle }); const barcodeMapWorksheet = Inputs.text({ label: "Barcode-map worksheet name", placeholder: "Leave blank to use the first worksheet", value: "", style: fullWidthInputStyle }); const barcodeColumn = Inputs.text({ label: "Barcode column in mapping file", value: "Barcode", style: fullWidthInputStyle }); const phageNameColumn = Inputs.text({ label: "Phage-name column in mapping file", value: "Phage Name", style: fullWidthInputStyle }); const keepUnmappedSamples = Inputs.toggle({ label: "Keep barcodes not found in the barcode map", value: true }); const lengthColumn = Inputs.text({ label: "Length column in assembly_info.txt", value: "length", style: fullWidthInputStyle }); const outputBaseName = Inputs.text({ label: "Output filename base", value: "combined_assembly_info", style: fullWidthInputStyle }); const overwriteOutput = Inputs.toggle({ label: "♻️ Overwrite existing output files", value: true }); const openResults = Inputs.toggle({ label: "📂 Open the output folder in Finder when finished", value: false }); const modeMessage = html`

`; const barcodeHelp = html`

Optional barcode-map format
The mapping workbook may contain columns such as Barcode and Phage Name.

Barcode     Phage Name
barcode005  Olympi
barcode006  Tadpole
barcode007  Seldom

When a map is supplied, the output keeps the original barcode in a separate Barcode column and writes the mapped phage name in the Sample column.

`; const textarea = html``; const copyBtn = html``; copyBtn.onclick = async () => { try { await navigator.clipboard.writeText(textarea.value); copyBtn.textContent = "✅ Copied!"; } catch (error) { textarea.select(); document.execCommand("copy"); copyBtn.textContent = "✅ Copied!"; } setTimeout(() => { copyBtn.textContent = "📋 Copy Mac script"; }, 1500); }; function removeOuterQuotes(value) { let text = String(value ?? "").trim(); while ( text.length >= 2 && ((text.startsWith('"') && text.endsWith('"')) || (text.startsWith("'") && text.endsWith("'"))) ) { text = text.slice(1, -1).trim(); } return text; } function shellSingleQuote(value) { return "'" + String(value ?? "").replace(/'/g, "'\\''") + "'"; } function pythonString(value) { return JSON.stringify(String(value ?? "")); } function pythonBoolean(value) { return value ? "True" : "False"; } function generateScript() { const defaultBasePath = "/Users/yourname/Desktop/Nanopore_Results/Run1/Sample1/assemblies"; const basePath = removeOuterQuotes(inputPath.value) || defaultBasePath; const mapPath = removeOuterQuotes(barcodeMapPath.value); const envName = envInput.value.trim() || "reads-assembly-core"; const mapWorksheet = barcodeMapWorksheet.value.trim(); const mapBarcodeHeader = barcodeColumn.value.trim() || "Barcode"; const mapPhageHeader = phageNameColumn.value.trim() || "Phage Name"; const requestedLengthColumn = lengthColumn.value.trim() || "length"; const requestedOutputBase = outputBaseName.value.trim() || "combined_assembly_info"; const keepAll = contigSelection.value.includes("Keep all contigs"); modeMessage.innerHTML = keepAll ? `Current selection: Keep all contigs.
The output will contain one row for every contig and will show the number of contigs found for each barcode.` : `Current selection: Keep only the longest contig for each barcode.
The output will contain one row per barcode and will show how many contigs were present before filtering.`; textarea.value = `bash <<'COMBINE_ASSEMBLY_MAC_SCRIPT' #!/usr/bin/env bash # Conda activation scripts on macOS may read unset backup variables. # Therefore, Bash nounset checking (-u) remains disabled until after # the requested Conda environment has been activated. set -Eeo pipefail trap 'status=$?; echo; echo "❌ Script failed at line $LINENO (exit $status)"; echo; echo "Press Enter to close..."; read -r _ /dev/null 2>&1; then CONDA_BASE="$(conda info --base 2>/dev/null || true)" if [ -n "$CONDA_BASE" ] && [ -f "$CONDA_BASE/etc/profile.d/conda.sh" ]; then CONDA_SH="$CONDA_BASE/etc/profile.d/conda.sh" fi fi # Conda activation and deactivation scripts sometimes reference variables # that are not defined. Keep nounset checking disabled while Conda runs. set +u if [ -n "$CONDA_SH" ]; then echo "✅ Conda initialization file:" echo " $CONDA_SH" . "$CONDA_SH" elif command -v conda >/dev/null 2>&1; then echo "✅ Using Conda from the current Terminal environment." eval "$(conda shell.bash hook)" else echo "❌ Conda could not be found." echo echo "Checked common locations including:" echo " $HOME/miniforge3" echo " $HOME/miniconda3" echo " $HOME/mambaforge" echo " $HOME/anaconda3" echo " /opt/miniconda3" echo " /opt/anaconda3" echo " Homebrew Miniforge locations" exit 1 fi echo echo "🔍 Checking for Conda environment: $ENV_NAME" if ! conda env list | awk 'NF && $1 !~ /^#/ {print $1}' | grep -Fxq "$ENV_NAME"; then echo "❌ Conda environment not found:" echo " $ENV_NAME" echo echo "Available Conda environments:" conda env list exit 1 fi echo "✅ Conda environment found." echo "▶ Activating environment: $ENV_NAME" if ! conda activate "$ENV_NAME"; then echo "❌ Could not activate Conda environment:" echo " $ENV_NAME" exit 1 fi echo "✅ Environment activated:" echo " \${CONDA_DEFAULT_ENV:-$ENV_NAME}" # Conda has finished activating. Enable strict unset-variable checking # for the remainder of the generated script. set -u echo echo "Python executable:" command -v python echo echo "Python version:" python --version echo echo "🔍 Checking required Python packages..." python - <<'PYTHON_PACKAGE_CHECK' import sys missing = [] for package in ("pandas", "openpyxl"): try: __import__(package) except ImportError: missing.append(package) if missing: print( "❌ Missing Python package(s): " + ", ".join(missing) ) print() print( "Install them in the selected environment with:" ) print( " conda install pandas openpyxl" ) sys.exit(1) print("✅ pandas and openpyxl are available.") PYTHON_PACKAGE_CHECK echo echo "▶ Combining assembly information..." python - <<'PYTHON_SCRIPT' from __future__ import annotations import re import subprocess import sys from pathlib import Path from typing import Optional base_dir = Path( ${pythonString(basePath)} ).expanduser() barcode_map_text = ${pythonString(mapPath)} barcode_map_path = ( Path(barcode_map_text).expanduser() if barcode_map_text else None ) barcode_map_worksheet = ${pythonString(mapWorksheet)} barcode_column_requested = ${pythonString(mapBarcodeHeader)} phage_column_requested = ${pythonString(mapPhageHeader)} length_column_requested = ${pythonString(requestedLengthColumn)} output_base_requested = ${pythonString(requestedOutputBase)} keep_all_contigs = ${pythonBoolean(keepAll)} keep_unmapped_samples = ${pythonBoolean(keepUnmappedSamples.value)} overwrite_output = ${pythonBoolean(overwriteOutput.value)} open_results = ${pythonBoolean(openResults.value)} try: import pandas as pd except ImportError: print( "❌ pandas is not installed in the selected " "Conda environment." ) sys.exit(1) try: import openpyxl from openpyxl.styles import ( Alignment, Font, PatternFill ) except ImportError: print( "❌ openpyxl is not installed in the selected " "Conda environment." ) sys.exit(1) def clean_text(value) -> str: if value is None: return "" try: if pd.isna(value): return "" except Exception: pass text = str(value).replace( "\\u00a0", " " ) return re.sub( r"\\s+", " ", text ).strip() def normalize_barcode(value) -> str: text = clean_text(value) if not text: return "" match = re.search( r"barcode[\\s_-]*0*([0-9]+)", text, flags=re.IGNORECASE ) if not match: match = re.fullmatch( r"0*([0-9]+)", text ) if not match: return "" return ( f"barcode{int(match.group(1)):03d}" ) def find_column( columns, requested_name: str ) -> Optional[str]: requested = clean_text( requested_name ).casefold() for column in columns: current = clean_text( column ).casefold() if current == requested: return column return None def sanitize_output_base( value: str ) -> str: text = clean_text(value) if not text: text = "combined_assembly_info" extensions = ( ".xlsx", ".xlsm", ".xls", ".tsv", ".txt" ) for extension in extensions: if text.lower().endswith( extension ): text = text[ : -len(extension) ] break text = re.sub( r'[<>:"/\\\\|?*]+', "_", text ) text = text.strip( " ._" ) return ( text or "combined_assembly_info" ) def read_assembly_info( info_path: Path ) -> pd.DataFrame: try: frame = pd.read_csv( info_path, sep="\\t", dtype=str, keep_default_na=False ) except Exception as error: raise RuntimeError( f"Could not read {info_path}: " f"{error}" ) from error # Flye normally uses tabs. If only one column was detected, # try splitting the file using general whitespace instead. if frame.shape[1] == 1: frame = pd.read_csv( info_path, sep=r"\\s+", dtype=str, keep_default_na=False ) frame.columns = [ clean_text(column) .lstrip("#") .strip() for column in frame.columns ] return frame def load_barcode_map( path: Optional[Path] ) -> dict[str, str]: if path is None: return {} if not path.is_file(): raise RuntimeError( "The barcode-map workbook " f"does not exist: {path}" ) sheet_name = ( barcode_map_worksheet if barcode_map_worksheet else 0 ) try: map_frame = pd.read_excel( path, sheet_name=sheet_name, dtype=str, engine="openpyxl" ) except Exception as error: raise RuntimeError( "Could not read the barcode-map " f"workbook {path}: {error}" ) from error barcode_column = find_column( map_frame.columns, barcode_column_requested ) phage_column = find_column( map_frame.columns, phage_column_requested ) available = ", ".join( str(column) for column in map_frame.columns ) if barcode_column is None: raise RuntimeError( "Barcode-map column " f"'{barcode_column_requested}' " "was not found. Available columns: " f"{available}" ) if phage_column is None: raise RuntimeError( "Phage-name column " f"'{phage_column_requested}' " "was not found. Available columns: " f"{available}" ) mapping: dict[str, str] = {} for _, row in map_frame.iterrows(): barcode = normalize_barcode( row[barcode_column] ) phage_name = clean_text( row[phage_column] ) if ( barcode and phage_name and barcode not in mapping ): mapping[barcode] = phage_name return mapping def choose_output_paths( stem: str ) -> tuple[Path, Path]: preferred_tsv = ( base_dir / f"{stem}.tsv" ) preferred_xlsx = ( base_dir / f"{stem}.xlsx" ) if overwrite_output: for path in ( preferred_tsv, preferred_xlsx ): if path.exists(): try: path.unlink() except PermissionError as error: raise RuntimeError( "Close the existing output " "file before overwriting it: " f"{path}" ) from error return ( preferred_tsv, preferred_xlsx ) if ( not preferred_tsv.exists() and not preferred_xlsx.exists() ): return ( preferred_tsv, preferred_xlsx ) number = 2 while True: candidate_tsv = ( base_dir / f"{stem}_{number}.tsv" ) candidate_xlsx = ( base_dir / f"{stem}_{number}.xlsx" ) if ( not candidate_tsv.exists() and not candidate_xlsx.exists() ): return ( candidate_tsv, candidate_xlsx ) number += 1 def format_excel_workbook( path: Path ) -> None: workbook = openpyxl.load_workbook( path ) worksheet = workbook[ "Assemblies" ] worksheet.freeze_panes = "A2" worksheet.auto_filter.ref = ( worksheet.dimensions ) header_fill = PatternFill( fill_type="solid", fgColor="D9EAD3" ) for cell in worksheet[1]: cell.font = Font( bold=True ) cell.fill = header_fill cell.alignment = Alignment( horizontal="center", vertical="center" ) for column_cells in worksheet.columns: maximum_length = 0 for cell in column_cells: value = ( "" if cell.value is None else str(cell.value) ) maximum_length = max( maximum_length, len(value) ) column_letter = ( column_cells[0].column_letter ) worksheet.column_dimensions[ column_letter ].width = min( max( maximum_length + 2, 11 ), 60 ) workbook.save(path) workbook.close() if not base_dir.is_dir(): raise RuntimeError( "Assembly folder does not exist: " f"{base_dir}" ) barcode_to_phage = load_barcode_map( barcode_map_path ) subfolders = sorted( ( path for path in base_dir.iterdir() if path.is_dir() ), key=lambda path: path.name.casefold() ) if not subfolders: raise RuntimeError( "No immediate subfolders were found in: " f"{base_dir}" ) frames = [] missing_info_files = [] excluded_unmapped_folders = [] source_order = 0 for folder in subfolders: info_path = ( folder / "assembly_info.txt" ) if not info_path.is_file(): missing_info_files.append( str(info_path) ) continue frame = read_assembly_info( info_path ) requested_length = find_column( frame.columns, length_column_requested ) if requested_length is None: available = ", ".join( str(column) for column in frame.columns ) raise RuntimeError( "Length column " f"'{length_column_requested}' " f"was not found in {info_path}. " "Available columns: " f"{available}" ) if requested_length != "length": frame = frame.rename( columns={ requested_length: "length" } ) # Avoid duplicate column names if assembly_info.txt already # contains one of the columns added by this script. reserved_columns = { "Folder": "Original Folder", "Barcode": "Original Barcode", "Sample": "Original Sample", "Number of Contigs": "Original Number of Contigs" } for old_name, new_name in ( reserved_columns.items() ): if old_name in frame.columns: frame = frame.rename( columns={ old_name: new_name } ) folder_name = folder.name standardized_barcode = ( normalize_barcode( folder_name ) ) barcode_value = ( standardized_barcode or folder_name ) if barcode_to_phage: mapped_name = ( barcode_to_phage.get( standardized_barcode, "" ) ) if mapped_name: sample_value = mapped_name elif keep_unmapped_samples: sample_value = folder_name else: excluded_unmapped_folders.append( folder_name ) continue else: sample_value = folder_name group_key = ( f"barcode:{standardized_barcode}" if standardized_barcode else ( "folder:" + folder_name.casefold() ) ) frame.insert( 0, "Sample", sample_value ) frame.insert( 0, "Barcode", barcode_value ) frame.insert( 0, "Folder", folder_name ) frame["_GroupKey"] = ( group_key ) frame["_SourceOrder"] = range( source_order, source_order + len(frame) ) source_order += len(frame) frames.append(frame) print( f"✅ Added: {info_path}" ) if not frames: raise RuntimeError( "No usable assembly_info.txt files " "were found in the immediate " "subfolders." ) combined = pd.concat( frames, ignore_index=True, sort=False ) combined["_NumericLength"] = pd.to_numeric( combined["length"] .astype(str) .str.replace( ",", "", regex=False ) .str.replace( "_", "", regex=False ) .str.strip(), errors="coerce" ) combined["Number of Contigs"] = ( combined.groupby( "_GroupKey", sort=False )["_GroupKey"] .transform("size") .astype(int) ) invalid_length_rows = int( combined[ "_NumericLength" ].isna().sum() ) if keep_all_contigs: result = combined.copy() mode_suffix = ( "all_contigs" ) else: valid_rows = combined[ combined[ "_NumericLength" ].notna() ].copy() if valid_rows.empty: raise RuntimeError( "No contig rows contained a " "numeric length, so the longest " "contig could not be selected." ) groups_with_valid_length = set( valid_rows["_GroupKey"] ) all_groups = set( combined["_GroupKey"] ) groups_without_valid_length = sorted( all_groups - groups_with_valid_length ) winner_indices = ( valid_rows.groupby( "_GroupKey", sort=False )["_NumericLength"] .idxmax() .tolist() ) result = combined.loc[ winner_indices ].copy() result = result.sort_values( "_SourceOrder", kind="stable" ) mode_suffix = ( "longest_contig_per_barcode" ) if groups_without_valid_length: print() print( "⚠️ Groups skipped because none " "of their contigs had a numeric " "length:" ) for group in ( groups_without_valid_length ): print( f" {group}" ) output_base = sanitize_output_base( output_base_requested ) output_stem = ( f"{output_base}_{mode_suffix}" ) output_tsv, output_xlsx = ( choose_output_paths( output_stem ) ) preferred_columns = [ "Folder", "Barcode", "Sample", "Number of Contigs" ] remaining_columns = [ column for column in result.columns if ( column not in preferred_columns and not str(column).startswith("_") ) ] result = result[ preferred_columns + remaining_columns ] result.to_csv( output_tsv, sep="\\t", index=False, lineterminator="\\n" ) with pd.ExcelWriter( output_xlsx, engine="openpyxl" ) as writer: result.to_excel( writer, index=False, sheet_name="Assemblies" ) format_excel_workbook( output_xlsx ) print() print( "============================================================" ) print( "✅ Assembly information combined successfully" ) print( "============================================================" ) print( "Assembly folders examined: " f"{len(subfolders)}" ) print( "assembly_info.txt files used: " f"{len(frames)}" ) print( "Input contig rows: " f"{len(combined)}" ) print( "Output rows: " f"{len(result)}" ) print( "Unique barcodes or folders: " f"{combined['_GroupKey'].nunique()}" ) print( "Rows with a non-numeric length: " f"{invalid_length_rows}" ) print( "Barcode mappings loaded: " f"{len(barcode_to_phage)}" ) print( "Mode: " + ( "keep all contigs" if keep_all_contigs else "longest contig per barcode" ) ) if missing_info_files: print() print( "⚠️ Missing assembly_info.txt files:" ) for missing_path in ( missing_info_files ): print( f" {missing_path}" ) if excluded_unmapped_folders: print() print( "⚠️ Folders excluded because they " "were absent from the barcode map:" ) for folder_name in ( excluded_unmapped_folders ): print( f" {folder_name}" ) print() print("Created:") print( f" {output_tsv}" ) print( f" {output_xlsx}" ) if open_results: subprocess.run( [ "open", str(base_dir) ], check=False ) PYTHON_SCRIPT echo echo "============================================================" echo "✅ Processing complete" echo "============================================================" echo echo "Output folder:" echo " $BASE_DIR" echo echo "Press Enter to close..." read -r _

Combine assembly information and select contigs — macOS

Assembly folders and environment

${inputPath} ${envInput}

Contig selection

${contigSelection} ${modeMessage}

Optional barcode-to-phage workbook

${barcodeMapPath} ${barcodeMapWorksheet} ${barcodeColumn} ${phageNameColumn} ${keepUnmappedSamples} ${barcodeHelp}

Output settings

${lengthColumn} ${outputBaseName} ${overwriteOutput} ${openResults}

Enter Mac paths beginning with /Users/.... Copy the generated code, paste it directly into Terminal, and press Enter. The generated code is enclosed in a Bash block so it can be pasted safely into the default macOS Zsh Terminal.

${copyBtn}

${textarea}

`; }3a:T43c9,viewof fastaFastqToBamGenerator3 = { const mode = Inputs.radio(["One Barcode", "Multiple Barcodes (Batch)"], { label: "1) Create BAM file for One Barcode or Multiple Barcodes (Batch)", value: "One Barcode" }); const condaEnvName = Inputs.text({ label: "Conda environment name", value: "reads-assembly-core", style: "width: 320px" }); const parentFolderPath = Inputs.text({ label: "Parent folder path (macOS path)", placeholder: "/Users/yourname/Desktop/Nanopore_Results", style: "width: 760px" }); const barcode = Inputs.text({ label: "Barcode name", value: "barcode001", style: "width: 220px" }); const singleFastqPath = Inputs.text({ label: "FASTQ file path (macOS path)", placeholder: "/Users/yourname/Desktop/Nanopore_Results/barcode001.fastq", style: "width: 760px" }); const singleFastaPath = Inputs.text({ label: "Reference FASTA file path (macOS path)", placeholder: "/Users/yourname/Desktop/Nanopore_Results/barcode001_assembly.fasta", style: "width: 760px" }); const singleOutPrefixPath = Inputs.text({ label: "Output prefix path (no extension, macOS path)", placeholder: "/Users/yourname/Desktop/Nanopore_Results/barcode001", style: "width: 760px" }); const readsGlob = Inputs.text({ label: "FASTQ glob template (batch, include {BARCODE})", value: "*{BARCODE}*.fastq", style: "width: 760px" }); const refRel = Inputs.text({ label: "FASTA template relative to parent folder (include {BARCODE})", value: "assemblies/{BARCODE}/{BARCODE}_assembly.fasta", style: "width: 760px" }); const outPrefixRel = Inputs.text({ label: "Output prefix template relative to parent folder (include {BARCODE})", value: "assemblies/{BARCODE}/{BARCODE}", style: "width: 760px" }); const threads = Inputs.range([1, 64], { label: "Threads", value: 4, step: 1 }); const formArea = html`

`; const singleSection = html`

`; const batchSection = html`

One Barcode
Enter one reference FASTA, one FASTQ, and one output prefix. Native macOS paths such as /Users/name/Desktop/file.fastq and paths beginning with ~/ are accepted.

`, barcode, singleFastqPath, singleFastaPath, singleOutPrefixPath ); batchSection.append( html`

Multiple Barcodes (Batch)
Enter the native macOS parent-folder path. The script looks for barcode* folders inside assemblies and substitutes each folder name for {BARCODE}.

`, parentFolderPath, readsGlob, refRel, outPrefixRel ); formArea.append( mode, condaEnvName, html`

${threads}

`, singleSection, batchSection ); updateModeVisibility(); } function updateModeVisibility() { const isBatch = mode.value === "Multiple Barcodes (Batch)"; singleSection.style.display = isBatch ? "none" : "grid"; batchSection.style.display = isBatch ? "grid" : "none"; } function updateScript() { const isBatch = mode.value === "Multiple Barcodes (Batch)"; const envName = String(condaEnvName.value ?? "").trim(); const oneBarcode = String(barcode.value ?? "").trim(); const oneFastq = cleanMacPath(singleFastqPath.value); const oneFasta = cleanMacPath(singleFastaPath.value); const oneOut = cleanMacPath(singleOutPrefixPath.value); const parentDir = cleanMacPath(parentFolderPath.value); const readsGlobValue = String(readsGlob.value ?? "").trim(); const refRelValue = String(refRel.value ?? "").trim(); const outPrefixRelValue = String(outPrefixRel.value ?? "").trim(); const lines = [ "bash <<'FASTA_FASTQ_TO_BAM_SCRIPT'", "#!/usr/bin/env bash", "# Generated by Observable", "# FASTQ + FASTA -> coordinate-sorted BAM on macOS", "", "set -uo pipefail", "", 'export PATH="/opt/homebrew/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:$PATH"', "", `CONDA_ENV_NAME=${shQuote(envName)}`, `THREADS=${shQuote(String(threads.value))}`, `MODE=${shQuote(isBatch ? "batch" : "single")}`, "", `ONE_BARCODE=${shQuote(oneBarcode)}`, `ONE_FASTQ=${shQuote(oneFastq)}`, `ONE_FASTA=${shQuote(oneFasta)}`, `ONE_OUT_PREFIX=${shQuote(oneOut)}`, "", `PARENT_DIR=${shQuote(parentDir)}`, `READS_GLOB_TEMPLATE=${shQuote(readsGlobValue)}`, `REF_TEMPLATE=${shQuote(refRelValue)}`, `OUT_TEMPLATE=${shQuote(outPrefixRelValue)}`, "", "pause_before_exit() {", " echo", ' echo "Press Enter to close..."', " read -r _ &2', " pause_before_exit", " exit 1", "}", "", "expand_path() {", ' local path_value="$1"', "", ' case "$path_value" in', ' "~")', ' printf "%s\\n" "$HOME"', " ;;", ' "~/"*)', ' printf "%s/%s\\n" "$HOME" "${path_value#\\~/}"', " ;;", " *)", ' printf "%s\\n" "$path_value"', " ;;", " esac", "}", "", "apply_template() {", ' local template_string="$1"', ' local barcode_name="$2"', ' printf "%s\\n" "${template_string//\\{BARCODE\\}/$barcode_name}"', "}", "", "initialize_conda() {", ' local conda_base=""', ' local candidate=""', "", " if command -v conda >/dev/null 2>&1; then", ' conda_base="$(conda info --base 2>/dev/null || true)"', " fi", "", ' if [ -z "$conda_base" ]; then', " for candidate in \\", ' "$HOME/miniconda3/bin/conda" \\', ' "$HOME/anaconda3/bin/conda" \\', ' "/opt/homebrew/Caskroom/miniconda/base/bin/conda" \\', ' "/usr/local/Caskroom/miniconda/base/bin/conda" \\', ' "/opt/homebrew/bin/conda" \\', ' "/usr/local/bin/conda"', " do", ' if [ -x "$candidate" ]; then', ' conda_base="$("$candidate" info --base 2>/dev/null || true)"', ' [ -n "$conda_base" ] && break', " fi", " done", " fi", "", ' [ -n "$conda_base" ] || return 1', ' [ -f "$conda_base/etc/profile.d/conda.sh" ] || return 1', "", ' source "$conda_base/etc/profile.d/conda.sh"', "}", "", 'if [ -z "$CONDA_ENV_NAME" ]; then', ' fatal "The Conda environment name is empty."', "fi", "", "if ! initialize_conda; then", ' fatal "Conda could not be located. Install Miniconda/Anaconda or initialize Conda for your shell."', "fi", "", 'if ! conda activate "$CONDA_ENV_NAME"; then', ' fatal "Could not activate Conda environment: $CONDA_ENV_NAME"', "fi", "", "hash -r", "", "if ! command -v minimap2 >/dev/null 2>&1; then", ' fatal "minimap2 was not found in Conda environment: $CONDA_ENV_NAME"', "fi", "", "if ! command -v samtools >/dev/null 2>&1; then", ' fatal "samtools was not found in Conda environment: $CONDA_ENV_NAME"', "fi", "", 'echo "============================================================"', 'echo " FASTQ + FASTA to coordinate-sorted BAM — macOS"', 'echo "============================================================"', 'echo "Conda environment: $CONDA_ENV_NAME"', 'echo "Threads: $THREADS"', "echo", "", "process_one() {", ' local barcode_name="$1"', ' local reference_fasta="$2"', ' local fastq_file="$3"', ' local output_prefix="$4"', ' local output_bam="${output_prefix}.sorted.bam"', "", ' echo "------------------------------------------------------------"', ' echo "Processing: $barcode_name"', ' echo "Reference: $reference_fasta"', ' echo "Reads: $fastq_file"', ' echo "BAM: $output_bam"', "", ' if [ -z "$reference_fasta" ] || [ ! -f "$reference_fasta" ]; then', ' echo "❌ Reference FASTA not found: $reference_fasta" >&2', " return 1", " fi", "", ' if [ -z "$fastq_file" ] || [ ! -f "$fastq_file" ]; then', ' echo "❌ FASTQ file not found: $fastq_file" >&2', " return 1", " fi", "", ' if [ -z "$output_prefix" ]; then', ' echo "❌ Output prefix is empty." >&2', " return 1", " fi", "", ' if ! mkdir -p "$(dirname "$output_prefix")"; then', ' echo "❌ Could not create the output directory." >&2', " return 1", " fi", "", ' if ! samtools faidx "$reference_fasta"; then', ' echo "⚠️ Warning: samtools could not create the FASTA index (.fai)." >&2', " fi", "", " if ! minimap2 \\", " -a \\", " -x map-ont \\", ' -t "$THREADS" \\', ' "$reference_fasta" \\', ' "$fastq_file" | \\', " samtools sort \\", ' -@ "$THREADS" \\', ' -o "$output_bam" \\', " -", " then", ' echo "❌ Alignment or BAM sorting failed for $barcode_name." >&2', ' rm -f "$output_bam"', " return 1", " fi", "", ' if ! samtools index -@ "$THREADS" "$output_bam"; then', ' echo "❌ BAM indexing failed for $barcode_name." >&2', " return 1", " fi", "", ' samtools flagstat -@ "$THREADS" "$output_bam" > "${output_prefix}.flagstat.txt" || true', ' samtools idxstats "$output_bam" > "${output_prefix}.idxstats.txt" || true', "", ' echo "✅ Finished: $barcode_name"', ' echo "BAM: $output_bam"', ' echo "BAI: ${output_bam}.bai"', ' echo "Flagstat: ${output_prefix}.flagstat.txt"', ' echo "Idxstats: ${output_prefix}.idxstats.txt"', " echo", " return 0", "}", "", 'ONE_FASTQ="$(expand_path "$ONE_FASTQ")"', 'ONE_FASTA="$(expand_path "$ONE_FASTA")"', 'ONE_OUT_PREFIX="$(expand_path "$ONE_OUT_PREFIX")"', 'PARENT_DIR="$(expand_path "$PARENT_DIR")"', "" ]; if (!isBatch) { lines.push( 'if [ -z "$ONE_BARCODE" ]; then', ' fatal "A barcode name is required."', "fi", "", 'if ! process_one "$ONE_BARCODE" "$ONE_FASTA" "$ONE_FASTQ" "$ONE_OUT_PREFIX"; then', " pause_before_exit", " exit 1", "fi", "", 'echo "============================================================"', 'echo "✅ BAM creation complete"', 'echo "============================================================"', "pause_before_exit", "FASTA_FASTQ_TO_BAM_SCRIPT" ); } else { lines.push( 'if [ -z "$PARENT_DIR" ] || [ ! -d "$PARENT_DIR" ]; then', ' fatal "Parent folder not found: $PARENT_DIR"', "fi", "", 'if [ -z "$READS_GLOB_TEMPLATE" ]; then', ' fatal "The FASTQ glob template is empty."', "fi", "", 'if [ -z "$REF_TEMPLATE" ]; then', ' fatal "The FASTA template is empty."', "fi", "", 'if [ -z "$OUT_TEMPLATE" ]; then', ' fatal "The output-prefix template is empty."', "fi", "", "shopt -s nullglob", 'barcode_directories=("$PARENT_DIR"/assemblies/barcode*/)', "shopt -u nullglob", "", 'if [ "${#barcode_directories[@]}" -eq 0 ]; then', ' fatal "No barcode folders were found under: $PARENT_DIR/assemblies"', "fi", "", "successful_count=0", "failed_count=0", "", 'for barcode_directory in "${barcode_directories[@]}"; do', ' barcode_name="$(basename "${barcode_directory%/}")"', ' reference_relative="$(apply_template "$REF_TEMPLATE" "$barcode_name")"', ' output_relative="$(apply_template "$OUT_TEMPLATE" "$barcode_name")"', ' reads_relative="$(apply_template "$READS_GLOB_TEMPLATE" "$barcode_name")"', "", ' reference_fasta="$PARENT_DIR/$reference_relative"', ' output_prefix="$PARENT_DIR/$output_relative"', ' fastq_pattern="$PARENT_DIR/$reads_relative"', "", ' fastq_file="$(compgen -G "$fastq_pattern" | LC_ALL=C sort | head -n 1 || true)"', ' match_count="$(compgen -G "$fastq_pattern" | wc -l | tr -d "[:space:]" || true)"', ' match_count="${match_count:-0}"', "", ' if [ "$match_count" -gt 1 ]; then', ' echo "⚠️ Multiple FASTQ files matched for $barcode_name."', ' echo " Pattern: $fastq_pattern"', ' echo " Using: $fastq_file"', " fi", "", ' if process_one "$barcode_name" "$reference_fasta" "$fastq_file" "$output_prefix"; then', " successful_count=$((successful_count + 1))", " else", " failed_count=$((failed_count + 1))", ' echo "⚠️ Skipping $barcode_name because of the error above."', " echo", " fi", "done", "", 'echo "============================================================"', 'echo "Batch summary"', 'echo "Successful barcodes: $successful_count"', 'echo "Failed barcodes: $failed_count"', 'echo "============================================================"', "", "pause_before_exit", "", 'if [ "$failed_count" -gt 0 ]; then', " exit 1", "fi", "", "FASTA_FASTQ_TO_BAM_SCRIPT" ); } textarea.value = lines.join("\n"); } buildForm(); const scriptInputs = [ mode, condaEnvName, parentFolderPath, barcode, singleFastqPath, singleFastaPath, singleOutPrefixPath, readsGlob, refRel, outPrefixRel, threads ]; scriptInputs.forEach((input) => { input.addEventListener("input", () => { if (input === mode) { updateModeVisibility(); } updateScript(); }); }); updateScript(); return html`

⬇ FASTQ + FASTA to sorted BAM — macOS script

${formArea}

Copy the generated script, paste it into the macOS Terminal, and press Enter. The generated Bash heredoc runs safely from zsh.

${copyBtn}

${textarea}

`; }3b:T41ed,viewof pharokkaInstallerMac = { const envInput = Inputs.text({ label: "🧪 Conda environment", value: "pharokka", placeholder: "pharokka", style: "width:100%" }); const versionInput = Inputs.text({ label: "🏷️ Pharokka version", value: "", placeholder: "Leave blank for latest available from Bioconda", style: "width:100%" }); const databaseDirInput = Inputs.text({ label: "📚 Database directory", value: "~/pharokka_databases", placeholder: "~/pharokka_databases", style: "width:100%" }); const installDatabasesInput = Inputs.toggle({ label: "Download or verify the Pharokka databases", value: true }); const recreateEnvironmentInput = Inputs.toggle({ label: "Recreate the Conda environment", value: false }); const textarea = html``; const copyButton = html``; const downloadButton = html``; const copyStatus = html``; const controlsPanel = html`

`; const controlsHeading = html`

Installer controls

`; const controlsBody = html`

`; controlsBody.append( envInput, versionInput, databaseDirInput, installDatabasesInput, recreateEnvironmentInput, html`

Apple Silicon Macs use a native osx-arm64 environment. Intel Macs use osx-64. If an existing environment has the wrong architecture, it is replaced automatically even when “Recreate the Conda environment” is turned off.

` ); controlsPanel.append(controlsHeading, controlsBody); const outputPanel = html`

`; const outputHeader = html`

Generated Mac Terminal code

${copyStatus} ${copyButton} ${downloadButton}

`; outputPanel.append(outputHeader, textarea); const contentGrid = html`

`; contentGrid.append(controlsPanel, outputPanel); const arrow = html`▶`; const summary = html`

${arrow}🧬 Pharokka installer generator — macOS

`; const detailsBody = html`

`; detailsBody.append(contentGrid); const details = html`

`; details.append(summary, detailsBody); details.addEventListener("toggle", () => { arrow.textContent = details.open ? "▼" : "▶"; }); const root = html`

`; root.append(details); let downloadableScript = ""; function shQuote(value) { return `'${String(value).replace(/'/g, `'\\''`)}'`; } function generateScript() { const envName = envInput.value.trim() || "pharokka"; const requestedVersion = versionInput.value.trim(); const databaseDir = databaseDirInput.value.trim() || "~/pharokka_databases"; const installDatabases = installDatabasesInput.value ? "yes" : "no"; const recreateEnvironment = recreateEnvironmentInput.value ? "yes" : "no"; const innerScript = `#!/usr/bin/env bash # Install Pharokka on macOS using the Mac's native architecture set -Eeuo pipefail ENV_NAME=${shQuote(envName)} PHAROKKA_VERSION=${shQuote(requestedVersion)} DB_DIR_INPUT=${shQuote(databaseDir)} INSTALL_DATABASES=${shQuote(installDatabases)} RECREATE_ENV=${shQuote(recreateEnvironment)} if [[ ! "$ENV_NAME" =~ ^[A-Za-z0-9._-]+$ ]]; then echo "❌ Invalid Conda environment name: $ENV_NAME" echo " Use only letters, numbers, periods, underscores, and hyphens." exit 1 fi if [ -n "$PHAROKKA_VERSION" ] && [[ ! "$PHAROKKA_VERSION" =~ ^[0-9A-Za-z._-]+$ ]]; then echo "❌ Invalid Pharokka version: $PHAROKKA_VERSION" exit 1 fi expand_user_path() { local raw="$1" case "$raw" in "~") printf '%s\\n' "$HOME" ;; "~/"*) # Remove the literal ~/ before adding $HOME. printf '%s/%s\\n' "$HOME" "\${raw:2}" ;; *) printf '%s\\n' "$raw" ;; esac } DB_DIR="$(expand_user_path "$DB_DIR_INPUT")" if [ -z "$DB_DIR" ]; then echo "❌ Database directory cannot be empty." exit 1 fi SAFE_ENV_NAME="$( printf '%s' "$ENV_NAME" | tr -c 'A-Za-z0-9._-' '_' )" LOG_FILE="$HOME/install_pharokka_\${SAFE_ENV_NAME}_mac.log" : > "$LOG_FILE" exec > >(tee -a "$LOG_FILE") 2>&1 finish() { local status="$1" trap - ERR echo echo "📄 Installation log:" echo " $LOG_FILE" echo echo "Press Enter to close..." read -r _ /dev/null 2>&1; then for conda_sh in \\ "$HOME/miniforge3/etc/profile.d/conda.sh" \\ "$HOME/mambaforge/etc/profile.d/conda.sh" \\ "$HOME/miniconda3/etc/profile.d/conda.sh" \\ "$HOME/anaconda3/etc/profile.d/conda.sh" \\ "/opt/miniconda3/etc/profile.d/conda.sh" \\ "/opt/anaconda3/etc/profile.d/conda.sh" \\ "/opt/homebrew/Caskroom/miniforge/base/etc/profile.d/conda.sh" \\ "/opt/homebrew/Caskroom/miniconda/base/etc/profile.d/conda.sh" \\ "/opt/homebrew/anaconda3/etc/profile.d/conda.sh" \\ "/usr/local/Caskroom/miniforge/base/etc/profile.d/conda.sh" \\ "/usr/local/Caskroom/miniconda/base/etc/profile.d/conda.sh" \\ "/usr/local/anaconda3/etc/profile.d/conda.sh"; do if [ -f "$conda_sh" ]; then # shellcheck disable=SC1090 source "$conda_sh" break fi done fi if ! command -v conda >/dev/null 2>&1; then echo "❌ Conda was not found." echo echo "Install Miniforge or Miniconda, reopen Terminal," echo "and run this installer again." finish 1 fi echo "✅ Conda found:" echo " $(command -v conda)" conda --version conda deactivate >/dev/null 2>&1 || true PACKAGE_SPEC="pharokka" if [ -n "$PHAROKKA_VERSION" ]; then PACKAGE_SPEC="pharokka=$PHAROKKA_VERSION" fi CONDA_COMMON=( --yes --override-channels --strict-channel-priority -c conda-forge -c bioconda ) if conda create --help 2>&1 | grep -q -- '--solver'; then CONDA_COMMON+=(--solver libmamba) echo "✅ Using Conda's libmamba solver." else echo "ℹ️ This Conda version does not expose --solver." echo " Conda's default solver will be used." fi env_exists() { conda env list | awk 'NF && $1 !~ /^#/ {print $1}' | grep -Fxq "$ENV_NAME" } detect_env_platform() { conda list \ -n "$ENV_NAME" \ --explicit \ 2>/dev/null | awk -F/ '/\\/(osx-arm64|osx-64)\\// { print $(NF-1) exit }' } NEED_RECREATE="no" if env_exists; then CURRENT_PLATFORM="$(detect_env_platform || true)" echo echo "🧪 Existing environment detected:" echo " $ENV_NAME" echo " Existing platform: \${CURRENT_PLATFORM:-unknown}" echo " Required platform: $TARGET_SUBDIR" if [ "$RECREATE_ENV" = "yes" ]; then echo "♻️ Environment recreation was requested." NEED_RECREATE="yes" elif [ -z "$CURRENT_PLATFORM" ]; then echo "⚠️ The existing environment architecture could not be determined." echo " It will be recreated for safety." NEED_RECREATE="yes" elif [ "$CURRENT_PLATFORM" != "$TARGET_SUBDIR" ]; then echo "⚠️ The existing environment uses the wrong architecture." echo " It will be recreated automatically." NEED_RECREATE="yes" fi fi if [ "$NEED_RECREATE" = "yes" ]; then echo echo "🗑️ Removing incompatible or outdated environment:" echo " $ENV_NAME" conda env remove \ -n "$ENV_NAME" \ --yes fi echo if env_exists; then echo "📦 Updating $PACKAGE_SPEC in the native environment..." CONDA_SUBDIR="$TARGET_SUBDIR" \ conda install \ -n "$ENV_NAME" \ "\${CONDA_COMMON[@]}" \ "$PACKAGE_SPEC" else echo "📦 Creating a native $TARGET_SUBDIR environment..." echo " Environment: $ENV_NAME" echo " Package: $PACKAGE_SPEC" CONDA_SUBDIR="$TARGET_SUBDIR" \ conda create \ -n "$ENV_NAME" \ "\${CONDA_COMMON[@]}" \ "$PACKAGE_SPEC" fi INSTALLED_PLATFORM="$(detect_env_platform || true)" echo echo "🔍 Checking the completed environment..." echo " Required platform: $TARGET_SUBDIR" echo " Installed platform: \${INSTALLED_PLATFORM:-unknown}" if [ "$INSTALLED_PLATFORM" != "$TARGET_SUBDIR" ]; then echo echo "❌ The Conda environment has the wrong architecture." echo " Required: $TARGET_SUBDIR" echo " Installed: \${INSTALLED_PLATFORM:-unknown}" finish 1 fi if [ "$TARGET_SUBDIR" = "osx-arm64" ] && conda list -n "$ENV_NAME" --explicit 2>/dev/null | grep -q '/osx-64/'; then echo echo "❌ Intel packages were detected in the Apple Silicon environment." echo " The environment is not safe to run." finish 1 fi CONDA_RUN=( conda run -n "$ENV_NAME" ) if conda run --help 2>&1 | grep -q -- '--no-capture-output'; then CONDA_RUN=( conda run --no-capture-output -n "$ENV_NAME" ) fi echo echo "🔍 Verifying the environment's Python architecture..." "\${CONDA_RUN[@]}" \ python -c ' import platform import sys print("✅ Python executable:", sys.executable) print("✅ Python version:", platform.python_version()) print("✅ Python architecture:", platform.machine()) ' echo echo "🔍 Verifying Pharokka..." if ! "\${CONDA_RUN[@]}" pharokka --version; then echo echo "❌ Pharokka could not start." echo " The environment was created for $TARGET_SUBDIR." echo echo "Installed packages:" conda list -n "$ENV_NAME" finish 1 fi "\${CONDA_RUN[@]}" \ pharokka --help \ >/dev/null "\${CONDA_RUN[@]}" \ pharokka run --help \ >/dev/null "\${CONDA_RUN[@]}" \ pharokka install --help \ >/dev/null echo echo "🔍 Verifying Pharokka dependencies..." "\${CONDA_RUN[@]}" bash -c ' set -e for command_name in \\ pharokka \\ mmseqs \\ mash \\ minced \\ aragorn \\ tRNAscan-SE; do if command -v "$command_name" >/dev/null 2>&1; then printf "✅ %-14s %s\\n" \\ "$command_name" \\ "$(command -v "$command_name")" else printf "❌ Missing dependency: %s\\n" "$command_name" exit 1 fi done ' if [ "$INSTALL_DATABASES" = "yes" ]; then echo echo "📚 Installing or checking the Pharokka databases..." echo " Destination:" echo " $DB_DIR" mkdir -p "$DB_DIR" "\${CONDA_RUN[@]}" \ pharokka install \ -o "$DB_DIR" DB_FILE_COUNT="$( find "$DB_DIR" \ -maxdepth 1 \ -type f | wc -l | tr -d ' ' )" DB_SIZE="$( du -sh "$DB_DIR" | awk '{print $1}' )" echo echo "✅ Database check completed." echo " Directory: $DB_DIR" echo " Files: $DB_FILE_COUNT" echo " Size: $DB_SIZE" else echo echo "⏭️ Database installation was skipped." echo echo "Install the databases later with:" echo echo " conda run -n $ENV_NAME pharokka install -o '$DB_DIR'" fi echo echo "============================================================" echo "✅ Pharokka installation complete" echo "============================================================" echo echo "Environment:" echo " $ENV_NAME" echo echo "Platform:" echo " $TARGET_SUBDIR" echo echo "Database directory:" echo " $DB_DIR" echo echo "Activate the environment later with:" echo " conda activate $ENV_NAME" echo echo "Check the installed version with:" echo " pharokka --version" echo echo "Example annotation command:" echo " pharokka run -i genome.fasta -o pharokka_output -d '$DB_DIR' -t 8" echo finish 0`; downloadableScript = innerScript; textarea.value = `bash <<'PHAROKKA_MAC_INSTALL_SCRIPT' ${innerScript} PHAROKKA_MAC_INSTALL_SCRIPT`; root.value = textarea.value; copyStatus.textContent = ""; } for (const control of [ envInput, versionInput, databaseDirInput, installDatabasesInput, recreateEnvironmentInput ]) { control.addEventListener("input", generateScript); control.addEventListener("change", generateScript); } copyButton.addEventListener("click", async () => { try { await navigator.clipboard.writeText(textarea.value); copyButton.textContent = "✅ Copied!"; copyStatus.textContent = ""; setTimeout(() => { copyButton.textContent = "📋 Copy Mac installer"; }, 1500); } catch (error) { textarea.focus(); textarea.select(); const copied = document.execCommand("copy"); copyStatus.textContent = copied ? "Copied" : "Select and copy manually"; } }); downloadButton.addEventListener("click", () => { const blob = new Blob([downloadableScript], { type: "text/x-shellscript;charset=utf-8" }); const url = URL.createObjectURL(blob); const link = document.createElement("a"); link.href = url; link.download = "install_pharokka_mac.sh"; document.body.appendChild(link); link.click(); link.remove(); setTimeout(() => { URL.revokeObjectURL(url); }, 1000); }); generateScript(); return root; }3c:T2211,viewof pharokkaRunnerMac = { const ph_mac = Inputs.text({ label: "Mac FASTA path", value: "~/Downloads/Seldom.fasta", placeholder: "/Users/yourname/Downloads/Seldom.fasta", style: "width:560px" }); const ph_env = Inputs.text({ label: "Conda environment", value: "pharokka", style: "width:320px" }); const ph_db = Inputs.text({ label: "Pharokka database directory", value: "~/pharokka_databases", placeholder: "~/pharokka_databases", style: "width:560px" }); const ph_open = Inputs.toggle({ label: "Open results in Finder", value: true }); const ph_threads = Inputs.range([1, 16], { value: 2, step: 1, label: "Threads" }); const textarea = html``; const copyBtn = html``; const dlBtn = html``; function shQuote(value) { return `'${String(value).replace(/'/g, `'\\''`)}'`; } function generateScript() { const macPath = ph_mac.value.trim(); const envName = ph_env.value.trim() || "pharokka"; const dbPath = ph_db.value.trim() || "~/pharokka_databases"; const safeThreads = Math.min( 16, Math.max(1, Number(ph_threads.value) || 2) ); const openFinder = ph_open.value; if (!macPath) { textarea.value = ""; copyBtn.disabled = true; dlBtn.disabled = true; return; } copyBtn.disabled = false; dlBtn.disabled = false; const innerScript = `#!/usr/bin/env bash # Run Pharokka on macOS set -Eeuo pipefail ENV_NAME=${shQuote(envName)} IN_FASTA_INPUT=${shQuote(macPath)} DB_INPUT=${shQuote(dbPath)} THREADS=${safeThreads} expand_user_path() { local raw="$1" case "$raw" in "~") printf '%s\\n' "$HOME" ;; "~/"*) printf '%s/%s\\n' "$HOME" "\${raw#~/}" ;; *) printf '%s\\n' "$raw" ;; esac } IN_FASTA="$(expand_user_path "$IN_FASTA_INPUT")" DB="$(expand_user_path "$DB_INPUT")" finish() { local status="$1" trap - ERR echo echo "Press Enter to close..." read -r _ >(tee -a "$LOG_FILE") 2>&1 echo "Input FASTA:" echo " $IN_FASTA" echo echo "Output directory:" echo " $OUT_DIR" echo echo "Database directory:" echo " $DB" echo echo "Conda environment:" echo " $ENV_NAME" echo echo "Threads:" echo " $THREADS" echo echo "🔎 Locating Conda..." export PATH="/opt/homebrew/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:\${PATH:-}" hash -r if ! command -v conda >/dev/null 2>&1; then for conda_sh in \\ "$HOME/miniforge3/etc/profile.d/conda.sh" \\ "$HOME/mambaforge/etc/profile.d/conda.sh" \\ "$HOME/miniconda3/etc/profile.d/conda.sh" \\ "$HOME/anaconda3/etc/profile.d/conda.sh" \\ "/opt/homebrew/Caskroom/miniforge/base/etc/profile.d/conda.sh" \\ "/opt/homebrew/Caskroom/miniconda/base/etc/profile.d/conda.sh" \\ "/opt/homebrew/anaconda3/etc/profile.d/conda.sh" \\ "/usr/local/Caskroom/miniforge/base/etc/profile.d/conda.sh" \\ "/usr/local/Caskroom/miniconda/base/etc/profile.d/conda.sh" \\ "/usr/local/anaconda3/etc/profile.d/conda.sh"; do if [ -f "$conda_sh" ]; then # shellcheck disable=SC1090 source "$conda_sh" break fi done fi if ! command -v conda >/dev/null 2>&1; then echo "❌ Conda was not found." echo echo "Install Pharokka using the separate Pharokka macOS installer first." finish 1 fi echo "✅ Conda found:" echo " $(command -v conda)" conda --version env_exists() { conda env list | awk 'NF && $1 !~ /^#/ {print $1}' | grep -Fxq "$ENV_NAME" } if ! env_exists; then echo echo "❌ Conda environment '$ENV_NAME' does not exist." echo echo "Run the Pharokka macOS installer before running this script." finish 1 fi CONDA_RUN=( conda run -n "$ENV_NAME" ) if conda run --help 2>&1 | grep -q -- '--no-capture-output'; then CONDA_RUN=( conda run --no-capture-output -n "$ENV_NAME" ) fi echo echo "🔍 Checking Pharokka..." "\${CONDA_RUN[@]}" pharokka --version if [ ! -d "$DB" ] || [ -z "$(find "$DB" -mindepth 1 -maxdepth 1 -print -quit 2>/dev/null)" ]; then echo echo "⬇ Pharokka databases were not found." echo " Downloading databases to:" echo " $DB" echo "\${CONDA_RUN[@]}" \ pharokka install \ -o "$DB" else echo echo "✅ Pharokka database directory is not empty." fi echo echo "🧬 Running Pharokka..." echo "\${CONDA_RUN[@]}" \ pharokka run \ -i "$IN_FASTA" \ -o "$OUT_DIR" \ -d "$DB" \ -t "$THREADS" \ --fast \ -g prodigal \ -f echo echo "============================================================" echo "✅ Pharokka annotation complete" echo "============================================================" echo echo "Results folder:" echo " $OUT_DIR" echo echo "Terminal log:" echo " $LOG_FILE" ${ openFinder ? `echo echo "📂 Opening the results folder in Finder..." if command -v open >/dev/null 2>&1; then open "$OUT_DIR" else echo "⚠️ The macOS open command was not found." fi` : `echo echo "ℹ️ Opening the results folder in Finder is disabled."` } finish 0`; textarea.value = `bash <<'PHAROKKA_MAC_RUN_SCRIPT' ${innerScript} PHAROKKA_MAC_RUN_SCRIPT`; } for (const control of [ph_mac, ph_env, ph_db, ph_open, ph_threads]) { control.addEventListener("input", generateScript); control.addEventListener("change", generateScript); } copyBtn.onclick = async () => { try { await navigator.clipboard.writeText(textarea.value); copyBtn.textContent = "✅ Copied!"; setTimeout(() => { copyBtn.textContent = "📋 Copy Pharokka Mac Script"; }, 1500); } catch (error) { textarea.focus(); textarea.select(); const copied = document.execCommand("copy"); copyBtn.textContent = copied ? "✅ Copied!" : "Copy manually"; setTimeout(() => { copyBtn.textContent = "📋 Copy Pharokka Mac Script"; }, 1500); } }; dlBtn.onclick = () => { const blob = new Blob([textarea.value], { type: "text/x-shellscript;charset=utf-8" }); const url = URL.createObjectURL(blob); const link = document.createElement("a"); link.href = url; link.download = "run_pharokka_mac.sh"; document.body.appendChild(link); link.click(); link.remove(); setTimeout(() => { URL.revokeObjectURL(url); }, 1000); }; generateScript(); return html`

▶ Pharokka annotation macOS script

${ph_mac} ${ph_env} ${ph_db} ${ph_open} ${ph_threads}

Enter a macOS FASTA path, copy the generated script, paste it into Terminal, and press Enter.

${textarea}

${copyBtn} ${dlBtn}

`; }3d:T22cf,viewof macRenameGenerator = { const parentFolderInput = Inputs.text({ label: "📁 Parent folder path (macOS)", placeholder: "/Users/kiera/Desktop/Nanopore_Results", style: "width: 600px" }); const renameModeInput = Inputs.select( new Map([ ["Rename files only", "files"], ["Rename folders only", "folders"], ["Rename files and folders", "both"] ]), { label: "Rename mode", value: "files" } ); const searchSubfoldersInput = Inputs.toggle({ label: "🔍 Search inside subfolders", value: true }); const findTextInput = Inputs.text({ label: "Text to replace", placeholder: "filtered_PL27f_", style: "width: 420px" }); const replaceTextInput = Inputs.text({ label: "Replace with", placeholder: "", style: "width: 420px" }); const outputBox = html``; const copyButton = html``; function shQuote(value) { return "'" + String(value).replace(/'/g, "'\"'\"'") + "'"; } function updateScript() { const rawParentFolder = parentFolderInput.value.trim(); const parentFolder = rawParentFolder === "/" ? "/" : rawParentFolder.replace(/\/+$/, ""); const mode = renameModeInput.value; const recursive = searchSubfoldersInput.value; const findText = findTextInput.value; const replaceText = replaceTextInput.value; if (!parentFolder || !findText) { outputBox.value = ""; copyButton.disabled = true; return; } copyButton.disabled = false; outputBox.value = `bash <<'MAC_RENAME_SCRIPT' #!/usr/bin/env bash # Rename matching files and/or folders beneath one parent folder on macOS. set -uo pipefail PARENT_FOLDER=${shQuote(parentFolder)} MODE=${shQuote(mode)} SEARCH_SUBFOLDERS=${recursive ? "true" : "false"} FIND_TEXT=${shQuote(findText)} REPLACE_WITH=${shQuote(replaceText)} pause_and_exit() { local status="$1" echo printf "Press Enter to close..." read -r _ '$REPLACE_WITH'" echo "" # Replace every literal occurrence of FIND_TEXT in one filename. # Quoting FIND_TEXT keeps characters such as *, ?, and [ literal. replace_literal() { local remaining="$1" local result="" local prefix="" while [[ "$remaining" == *"$FIND_TEXT"* ]]; do prefix="\${remaining%%"$FIND_TEXT"*}" result="\${result}\${prefix}\${REPLACE_WITH}" remaining="\${remaining#*"$FIND_TEXT"}" done printf '%s%s' "$result" "$remaining" } rename_matching_items() { local item_type="$1" local found_count=0 local renamed_count=0 local skipped_count=0 local item="" local name="" local parent_path="" local new_name="" local new_path="" local -a find_args if [ "$item_type" = "files" ]; then if [ "$SEARCH_SUBFOLDERS" = "true" ]; then find_args=( "$PARENT_FOLDER" "-type" "f" "-print0" ) else # Portable macOS find expression for immediate children only. find_args=( "$PARENT_FOLDER" "!" "-path" "$PARENT_FOLDER" "-prune" "-type" "f" "-print0" ) fi elif [ "$item_type" = "folders" ]; then if [ "$SEARCH_SUBFOLDERS" = "true" ]; then # -depth lists nested folders before their parents. # This prevents renaming a parent before its child folders. find_args=( "$PARENT_FOLDER" "-depth" "-type" "d" "!" "-path" "$PARENT_FOLDER" "-print0" ) else find_args=( "$PARENT_FOLDER" "!" "-path" "$PARENT_FOLDER" "-prune" "-type" "d" "-print0" ) fi else echo "❌ ERROR: Unknown item type: $item_type" return 1 fi while IFS= read -r -d '' item; do name="\${item##*/}" if [[ "$name" != *"$FIND_TEXT"* ]]; then continue fi found_count=$((found_count + 1)) new_name="$(replace_literal "$name")" if [ "$new_name" = "$name" ]; then continue fi if [ -z "$new_name" ] || [ "$new_name" = "." ] || [ "$new_name" = ".." ]; then echo "" echo "OLD: $item" echo "SKIP: The resulting name would be invalid." skipped_count=$((skipped_count + 1)) continue fi parent_path="\${item%/*}" new_path="$parent_path/$new_name" echo "" echo "OLD: $item" echo "NEW: $new_path" if [ -e "$new_path" ] || [ -L "$new_path" ]; then echo "SKIP: A file or folder with the target name already exists." skipped_count=$((skipped_count + 1)) continue fi if mv "$item" "$new_path"; then echo "✅ RENAMED" renamed_count=$((renamed_count + 1)) else echo "❌ FAILED" skipped_count=$((skipped_count + 1)) fi done < <(find "\${find_args[@]}") echo "" if [ "$found_count" -eq 0 ]; then echo "No matching $item_type found." else echo "$item_type summary:" echo " Matching items: $found_count" echo " Renamed: $renamed_count" echo " Skipped/failed: $skipped_count" fi } case "$MODE" in files) rename_matching_items "files" ;; folders) rename_matching_items "folders" ;; both) rename_matching_items "files" rename_matching_items "folders" ;; *) echo "❌ ERROR: Unknown mode: $MODE" pause_and_exit 1 ;; esac echo "" echo "============================================================" echo "✅ Renaming complete" echo "============================================================" pause_and_exit 0 MAC_RENAME_SCRIPT `; } [ parentFolderInput, renameModeInput, searchSubfoldersInput, findTextInput, replaceTextInput ].forEach((input) => { input.addEventListener("input", updateScript); }); copyButton.onclick = async () => { await navigator.clipboard.writeText(outputBox.value); copyButton.textContent = "✅ Copied!"; setTimeout(() => { copyButton.textContent = "📋 Copy Mac Script"; }, 1500); }; updateScript(); return html`

⬇ Mac rename files/folders script

${parentFolderInput} ${renameModeInput} ${searchSubfoldersInput} ${findTextInput} ${replaceTextInput}

Enter a macOS path such as /Users/kiera/Desktop/Nanopore_Results. Copy the generated script, paste it into Terminal, and press Enter.

${copyButton}

${outputBox}

`; }3e:T358d,viewof nanoCompGithubMacInstaller = { const envInput = Inputs.text({ label: "🧪 Conda environment name", value: "reads-assembly-core", placeholder: "reads-assembly-core", style: "width:100%; box-sizing:border-box;" }); const repoInput = Inputs.text({ label: "GitHub repository", value: "https://github.com/wdecoster/nanocomp.git", style: "width:100%; box-sizing:border-box;" }); const refInput = Inputs.text({ label: "Git branch or tag", value: "master", placeholder: "master", style: "width:100%; box-sizing:border-box;" }); const pythonInput = Inputs.text({ label: "Python version for a new environment", value: "3.11", placeholder: "3.11", style: "width:100%; box-sizing:border-box;" }); const createEnvToggle = Inputs.toggle({ label: "Create the Conda environment if it does not exist", value: true }); /* * Left-side input controls. */ const controlsPanel = html`

⚙️ Installer settings

`; const controlsGrid = controlsPanel.querySelector(".nanocomp-controls-grid"); controlsGrid.append( envInput, repoInput, refInput, pythonInput, createEnvToggle ); /* * Right-side generated script. * * This textarea is a direct grid item beside the controls panel. * CSS grid stretching makes it the same height as the controls panel. */ const textarea = html``; const copyBtn = html``; const downloadBtn = html``; const status = html``; const buttonRow = html`

`; buttonRow.append(copyBtn, downloadBtn, status); const note = html`

Paste the generated block into macOS Terminal. It installs NanoComp directly from the selected GitHub branch or tag into the selected Conda environment.

`; /* * Two-column layout: * * Left = user controls * Right = generated shell script */ const mainGrid = html`

`; mainGrid.append(controlsPanel, textarea); /* * Everything inside this content section is hidden when the outer * details element is collapsed. */ const collapsibleContent = html`

`; collapsibleContent.append(mainGrid, buttonRow, note); /* * Outer collapsible section for the entire installer generator. */ const installerDetails = html`

🧬 NanoComp GitHub Installer for macOS

`; installerDetails.append(collapsibleContent); /* * Styles for the complete interface. */ const styles = html``; const container = html`

`; container.append(styles, installerDetails); function shQuote(value) { return `'${String(value).replace(/'/g, `'\\''`)}'`; } function generateScript() { const envName = envInput.value.trim() || "reads-assembly-core"; const repoUrl = repoInput.value.trim() || "https://github.com/wdecoster/nanocomp.git"; const gitRef = refInput.value.trim() || "master"; const pythonVersion = pythonInput.value.trim() || "3.11"; const createMissingEnvironment = createEnvToggle.value ? 1 : 0; const innerScript = `#!/usr/bin/env bash set -Eeuo pipefail trap 'status=$?; echo; echo "❌ NanoComp installation failed at line $LINENO (exit $status)."; exit $status' ERR ENV_NAME=${shQuote(envName)} REPO_URL=${shQuote(repoUrl)} GIT_REF=${shQuote(gitRef)} PYTHON_VERSION=${shQuote(pythonVersion)} CREATE_ENV_IF_MISSING=${createMissingEnvironment} WORKDIR="" cleanup() { if [ -n "$WORKDIR" ] && [ -d "$WORKDIR" ]; then rm -rf "$WORKDIR" fi } trap cleanup EXIT echo "============================================================" echo " NanoComp GitHub installer for macOS" echo "============================================================" echo "Conda environment : $ENV_NAME" echo "GitHub repository : $REPO_URL" echo "Git branch/tag : $GIT_REF" echo # Locate Conda even when the current shell has not initialized it. if ! command -v conda >/dev/null 2>&1; then for candidate in \\ "$HOME/miniconda3/bin/conda" \\ "$HOME/anaconda3/bin/conda" \\ "/opt/miniconda3/bin/conda" \\ "/opt/anaconda3/bin/conda" \\ "/opt/homebrew/Caskroom/miniconda/base/bin/conda"; do if [ -x "$candidate" ]; then export PATH="$(dirname "$candidate"):$PATH" break fi done fi if ! command -v conda >/dev/null 2>&1; then echo "❌ Conda was not found." echo echo "Install Miniconda or Anaconda, then run this installer again." exit 1 fi CONDA_BASE="$(conda info --base)" # Load Conda functions into this shell. # shellcheck disable=SC1091 source "$CONDA_BASE/etc/profile.d/conda.sh" # Determine whether the requested environment already exists. if [ "$ENV_NAME" = "base" ]; then ENV_PATH="$CONDA_BASE" else ENV_PATH="$( conda env list --json | "$CONDA_BASE/bin/python" -c ' import json import os import sys name = sys.argv[1] paths = json.load(sys.stdin).get("envs", []) print( next( ( path for path in paths if os.path.basename(path.rstrip(os.sep)) == name ), "" ) ) ' "$ENV_NAME" )" fi if [ -z "$ENV_PATH" ]; then if [ "$CREATE_ENV_IF_MISSING" -eq 1 ]; then echo "🧪 Creating Conda environment: $ENV_NAME" conda create \\ --yes \\ --name "$ENV_NAME" \\ --channel conda-forge \\ "python=$PYTHON_VERSION" \\ pip else echo "❌ Conda environment '$ENV_NAME' does not exist." echo echo "Enable:" echo " Create the Conda environment if it does not exist" echo echo "Then regenerate the installer." exit 1 fi else echo "✅ Found Conda environment: $ENV_NAME" fi if ! conda run \\ --name "$ENV_NAME" \\ python --version \\ >/dev/null 2>&1; then echo "❌ Python could not run in Conda environment '$ENV_NAME'." exit 1 fi echo echo "📦 Updating Python packaging tools..." conda run \\ --name "$ENV_NAME" \\ python -m pip install \\ --upgrade \\ pip \\ setuptools \\ wheel # Use the system Git installation when available. # Otherwise install Git inside the Conda environment. if command -v git >/dev/null 2>&1; then GIT_COMMAND=(git) else echo echo "📦 Git was not found." echo "Installing Git in Conda environment: $ENV_NAME" conda install \\ --yes \\ --name "$ENV_NAME" \\ --channel conda-forge \\ git GIT_COMMAND=( conda run --name "$ENV_NAME" git ) fi WORKDIR="$(mktemp -d "\${TMPDIR:-/tmp}/nanocomp-install.XXXXXX")" SRC_DIR="$WORKDIR/NanoComp" echo echo "⬇️ Cloning NanoComp from GitHub..." "\${GIT_COMMAND[@]}" clone \\ --depth 1 \\ --branch "$GIT_REF" \\ "$REPO_URL" \\ "$SRC_DIR" COMMIT_SHA="$( "\${GIT_COMMAND[@]}" \\ -C "$SRC_DIR" \\ rev-parse HEAD )" COMMIT_SHORT="$( "\${GIT_COMMAND[@]}" \\ -C "$SRC_DIR" \\ rev-parse --short HEAD )" echo echo "🧬 Installing NanoComp from commit $COMMIT_SHORT..." conda run \\ --name "$ENV_NAME" \\ python -m pip install \\ --upgrade \\ --upgrade-strategy only-if-needed \\ "$SRC_DIR" echo echo "🔎 Verifying the NanoComp installation..." INSTALLED_VERSION="$( conda run \\ --name "$ENV_NAME" \\ python -c \\ 'from importlib.metadata import version; print(version("nanocomp"))' | tail -n 1 )" conda run \\ --name "$ENV_NAME" \\ NanoComp --version conda run \\ --name "$ENV_NAME" \\ python -c \\ 'import nanocomp; print("✅ NanoComp Python import succeeded")' echo echo "============================================================" echo "✅ NanoComp installation completed" echo "Environment : $ENV_NAME" echo "Installed version : $INSTALLED_VERSION" echo "Git commit : $COMMIT_SHA" echo "============================================================" echo echo "To use NanoComp:" echo echo " conda activate $ENV_NAME" echo " NanoComp --help" `; textarea.value = `bash <<'NANOCOMP_GITHUB_INSTALLER'\n` + `${innerScript.trimEnd()}\n` + `NANOCOMP_GITHUB_INSTALLER`; status.textContent = `Ready: GitHub ${gitRef} → Conda environment ${envName}`; container.dispatchEvent( new Event("input", { bubbles: true }) ); } for (const control of [ envInput, repoInput, refInput, pythonInput, createEnvToggle ]) { control.addEventListener("input", generateScript); } copyBtn.addEventListener("click", async () => { try { await navigator.clipboard.writeText(textarea.value); status.textContent = "✅ Installer copied to the clipboard"; } catch (error) { textarea.focus(); textarea.select(); document.execCommand("copy"); status.textContent = "✅ Installer copied to the clipboard"; } }); downloadBtn.addEventListener("click", () => { const blob = new Blob([`${textarea.value}\n`], { type: "text/x-shellscript;charset=utf-8" }); const url = URL.createObjectURL(blob); const link = document.createElement("a"); link.href = url; link.download = "install_nanocomp_from_github_mac.sh"; document.body.append(link); link.click(); link.remove(); setTimeout(() => URL.revokeObjectURL(url), 0); status.textContent = "✅ Installer downloaded"; }); Object.defineProperty(container, "value", { get: () => textarea.value }); generateScript(); return container; }3f:T41cc,viewof nanoPlotGitHubInstaller = { // ------------------------------------------------------------ // User-input controls // ------------------------------------------------------------ const envInput = Inputs.text({ label: "🧪 Conda environment name", value: "reads-assembly-core", placeholder: "reads-assembly-core", style: "width:100%; box-sizing:border-box;" }); const refInput = Inputs.text({ label: "🌿 GitHub branch, tag, or commit", value: "master", placeholder: "master", style: "width:100%; box-sizing:border-box;" }); const pythonInput = Inputs.select(["3.10", "3.11", "3.12"], { label: "🐍 Python version for a new environment", value: "3.11", style: "width:100%;" }); const createEnvInput = Inputs.toggle({ label: "Create the Conda environment if it does not exist", value: true }); const upgradeToolsInput = Inputs.toggle({ label: "Update pip, setuptools, and wheel", value: true }); const forceReinstallInput = Inputs.toggle({ label: "Force reinstall NanoPlot", value: false }); // ------------------------------------------------------------ // Generated-code output // ------------------------------------------------------------ const textarea = html` `; const copyButton = html` `; const status = html` `; // ------------------------------------------------------------ // Left-side controls panel // ------------------------------------------------------------ const controlsPanel = html`

⚙️ Installer settings

${envInput} ${refInput} ${pythonInput} ${createEnvInput} ${upgradeToolsInput} ${forceReinstallInput}

Installation source
https://github.com/wdecoster/NanoPlot.git

The default GitHub branch is master. You can also enter a release tag or commit hash.

`; // ------------------------------------------------------------ // Right-side script panel // ------------------------------------------------------------ const outputPanel = html`

🍎 Generated macOS installer

${copyButton} ${status}

${textarea}

`; // ------------------------------------------------------------ // Responsive two-column layout // ------------------------------------------------------------ const responsiveStyle = html` `; // ------------------------------------------------------------ // Collapsible outer window // ------------------------------------------------------------ const container = html`

${responsiveStyle}

🧬 NanoPlot GitHub Installer for macOS

${controlsPanel} ${outputPanel}

`; // ------------------------------------------------------------ // Shell-safe quoting // ------------------------------------------------------------ function shQuote(value) { return "'" + String(value).replace(/'/g, "'\\''") + "'"; } // ------------------------------------------------------------ // Generate the macOS installation script // ------------------------------------------------------------ function generateScript() { const envName = String(envInput.value ?? "").trim() || "reads-assembly-core"; const gitRef = String(refInput.value ?? "").trim() || "master"; const pythonVersion = String(pythonInput.value ?? "").trim() || "3.11"; if (!/^[A-Za-z0-9._-]+$/.test(envName)) { textarea.value = `# ERROR The Conda environment name may contain only: • letters • numbers • periods • underscores • hyphens Please update the environment name in the settings.`; status.textContent = "❌ Invalid environment name"; status.style.color = "#b00020"; container.value = ""; container.dispatchEvent(new Event("input", { bubbles: true })); return; } if (!gitRef) { textarea.value = `# ERROR Enter a GitHub branch, release tag, or commit hash.`; status.textContent = "❌ GitHub reference required"; status.style.color = "#b00020"; container.value = ""; container.dispatchEvent(new Event("input", { bubbles: true })); return; } const createEnvironmentFlag = createEnvInput.value ? 1 : 0; const updateBuildToolsBlock = upgradeToolsInput.value ? `echo echo "⬆️ Updating pip, setuptools, and wheel..." "$CONDA_EXE" run --name "$ENV_NAME" \\ python -m pip install \\ --upgrade \\ pip \\ setuptools \\ wheel` : `echo echo "ℹ️ Skipping the pip build-tool update."`; const installCommand = forceReinstallInput.value ? `"$CONDA_EXE" run --name "$ENV_NAME" \\ python -m pip install \\ --upgrade \\ --force-reinstall \\ --no-cache-dir \\ "$NANOPLOT_SOURCE"` : `"$CONDA_EXE" run --name "$ENV_NAME" \\ python -m pip install \\ --upgrade \\ "$NANOPLOT_SOURCE"`; const script = `bash <<'NANOPLOT_INSTALLER' #!/usr/bin/env bash set -Eeuo pipefail # ============================================================ # NanoPlot GitHub installer for macOS # # Repository: # https://github.com/wdecoster/NanoPlot # ============================================================ ENV_NAME=${shQuote(envName)} PYTHON_VERSION=${shQuote(pythonVersion)} GIT_REF=${shQuote(gitRef)} REPOSITORY_URL='https://github.com/wdecoster/NanoPlot.git' CREATE_ENV_IF_MISSING=${createEnvironmentFlag} export PIP_DISABLE_PIP_VERSION_CHECK=1 export PYTHONNOUSERSITE=1 export GIT_TERMINAL_PROMPT=0 trap 'status=$?; echo; echo "❌ NanoPlot installation failed at line $LINENO (exit $status)."; exit $status' ERR echo echo "============================================================" echo " NanoPlot GitHub Installer" echo "============================================================" echo echo "Conda environment : $ENV_NAME" echo "Python version : $PYTHON_VERSION" echo "GitHub reference : $GIT_REF" echo "Repository : $REPOSITORY_URL" echo # ------------------------------------------------------------ # Confirm that this is macOS # ------------------------------------------------------------ if [[ "$(uname -s)" != "Darwin" ]]; then echo "❌ This installer is intended for macOS." echo "Detected operating system: $(uname -s)" exit 1 fi # ------------------------------------------------------------ # Locate Conda # ------------------------------------------------------------ find_conda() { if command -v conda >/dev/null 2>&1; then command -v conda return 0 fi for candidate in \\ "/opt/miniconda3/bin/conda" \\ "/opt/anaconda3/bin/conda" \\ "/usr/local/miniconda3/bin/conda" \\ "/usr/local/anaconda3/bin/conda" \\ "$HOME/miniconda3/bin/conda" \\ "$HOME/anaconda3/bin/conda" \\ "$HOME/miniforge3/bin/conda" \\ "$HOME/mambaforge/bin/conda" do if [[ -x "$candidate" ]]; then printf '%s\\n' "$candidate" return 0 fi done return 1 } if ! CONDA_EXE="$(find_conda)"; then echo "❌ Conda could not be found." echo echo "Install Miniconda or Miniforge, then run this installer again." echo echo "Common expected location:" echo " /opt/miniconda3/bin/conda" exit 1 fi echo "✅ Conda found:" echo " $CONDA_EXE" echo "$CONDA_EXE" --version # ------------------------------------------------------------ # Create or locate the requested environment # ------------------------------------------------------------ if "$CONDA_EXE" run --name "$ENV_NAME" \\ python -c "import sys" \\ >/dev/null 2>&1 then echo echo "✅ Conda environment already exists:" echo " $ENV_NAME" else if [[ "$CREATE_ENV_IF_MISSING" -eq 1 ]]; then echo echo "🧪 Creating Conda environment:" echo " $ENV_NAME" echo "$CONDA_EXE" create \\ --yes \\ --name "$ENV_NAME" \\ --channel conda-forge \\ "python=$PYTHON_VERSION" \\ pip \\ git else echo echo "❌ The Conda environment does not exist:" echo " $ENV_NAME" echo echo "Enable the option to create the environment, or choose an" echo "environment that already exists." exit 1 fi fi # ------------------------------------------------------------ # Confirm Python and pip # ------------------------------------------------------------ echo echo "🐍 Python in the selected environment:" "$CONDA_EXE" run --name "$ENV_NAME" \\ python --version if ! "$CONDA_EXE" run --name "$ENV_NAME" \\ python -m pip --version \\ >/dev/null 2>&1 then echo echo "📦 Installing pip..." "$CONDA_EXE" install \\ --yes \\ --name "$ENV_NAME" \\ --channel conda-forge \\ pip fi # ------------------------------------------------------------ # Ensure Git is available # ------------------------------------------------------------ if ! "$CONDA_EXE" run --name "$ENV_NAME" \\ git --version \\ >/dev/null 2>&1 then echo echo "📦 Installing Git into the Conda environment..." "$CONDA_EXE" install \\ --yes \\ --name "$ENV_NAME" \\ --channel conda-forge \\ git fi echo echo "✅ Git is available:" "$CONDA_EXE" run --name "$ENV_NAME" \\ git --version # ------------------------------------------------------------ # Update Python installation tools # ------------------------------------------------------------ ${updateBuildToolsBlock} # ------------------------------------------------------------ # Install NanoPlot directly from GitHub # ------------------------------------------------------------ NANOPLOT_SOURCE="git+$REPOSITORY_URL@$GIT_REF" echo echo "📥 Installing NanoPlot directly from GitHub..." echo echo "Source:" echo " $NANOPLOT_SOURCE" echo ${installCommand} # ------------------------------------------------------------ # Verify the installation # ------------------------------------------------------------ echo echo "🔍 Verifying NanoPlot..." "$CONDA_EXE" run --name "$ENV_NAME" \\ python -c "import nanoplot; print('NanoPlot Python package imported successfully.')" echo echo "Installed NanoPlot version:" "$CONDA_EXE" run --name "$ENV_NAME" \\ NanoPlot --version echo echo "NanoPlot executable:" "$CONDA_EXE" run --name "$ENV_NAME" \\ python -c 'import shutil; print(shutil.which("NanoPlot") or "NanoPlot executable not found")' # ------------------------------------------------------------ # Completion information # ------------------------------------------------------------ CONDA_BASE="$("$CONDA_EXE" info --base)" echo echo "============================================================" echo " ✅ NanoPlot installation completed successfully" echo "============================================================" echo echo "Environment:" echo " $ENV_NAME" echo echo "To activate the environment in a new Terminal window:" echo echo " source \\"$CONDA_BASE/etc/profile.d/conda.sh\\"" echo " conda activate \\"$ENV_NAME\\"" echo echo "Check the installation:" echo echo " NanoPlot --version" echo " NanoPlot --help" echo echo "Example FASTQ command:" echo echo " NanoPlot \\\\" echo " --fastq \\"/path/to/reads.fastq.gz\\" \\\\" echo " --outdir \\"/path/to/NanoPlot_results\\" \\\\" echo " --threads 8" echo echo "You can also run NanoPlot without activating the environment:" echo echo " \\"$CONDA_EXE\\" run --name \\"$ENV_NAME\\" NanoPlot --help" echo NANOPLOT_INSTALLER`; textarea.value = script; status.textContent = "✅ macOS installer generated"; status.style.color = "#147a32"; container.value = script; container.dispatchEvent(new Event("input", { bubbles: true })); } // ------------------------------------------------------------ // Copy button // ------------------------------------------------------------ copyButton.addEventListener("click", async () => { try { await navigator.clipboard.writeText(textarea.value); status.textContent = "✅ Installer copied"; status.style.color = "#147a32"; } catch (error) { textarea.focus(); textarea.select(); const copied = document.execCommand("copy"); if (copied) { status.textContent = "✅ Installer copied"; status.style.color = "#147a32"; } else { status.textContent = "❌ Copy failed — select the code manually"; status.style.color = "#b00020"; } } }); // ------------------------------------------------------------ // Regenerate when a setting changes // ------------------------------------------------------------ for (const control of [ envInput, refInput, pythonInput, createEnvInput, upgradeToolsInput, forceReinstallInput ]) { control.addEventListener("input", generateScript); } generateScript(); return container; }40:T3b54,viewof filtlongInstaller = { const envInput = Inputs.text({ label: "🧪 Conda environment name", value: "reads-assembly-core", style: "width: 100%; box-sizing: border-box;" }); const gitRefInput = Inputs.text({ label: "🌿 Git branch, tag, or commit", value: "main", placeholder: "main", style: "width: 100%; box-sizing: border-box;" }); const createEnvInput = Inputs.toggle({ label: "➕ Create Conda environment if missing", value: true }); const forceInput = Inputs.toggle({ label: "♻️ Replace existing Filtlong executable", value: true }); const textarea = html``; const buttonStyle = ` padding: 0.5em 0.85em; border: 1px solid #bbb; border-radius: 6px; background: #f7f7f7; cursor: pointer; font-size: 0.9em; `; const copyBtn = html``; const openRepoBtn = html``; const status = html``; function shQuote(value) { return `'${String(value).replace(/'/g, `'\\''`)}'`; } function generateScript() { const envName = envInput.value.trim() || "reads-assembly-core"; const gitRef = gitRefInput.value.trim() || "main"; const createEnv = Boolean(createEnvInput.value); const forceReinstall = Boolean(forceInput.value); const innerScript = `#!/usr/bin/env bash set -Eeuo pipefail ENV_NAME=${shQuote(envName)} GIT_REF=${shQuote(gitRef)} CREATE_ENV=${createEnv ? "1" : "0"} FORCE_REINSTALL=${forceReinstall ? "1" : "0"} REPO_URL="https://github.com/rrwick/Filtlong.git" WORKDIR="" ENV_PREFIX="" DESTINATION="" CONDA_BIN="" CONDA_BASE="" trap 'status=$?; echo; echo "ERROR: Filtlong installation failed at line $LINENO (exit $status)"; exit $status' ERR cleanup() { if [ -n "$WORKDIR" ] && [ -d "$WORKDIR" ]; then rm -rf "$WORKDIR" fi } trap cleanup EXIT export PATH="/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/usr/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:$PATH" echo echo "============================================================" echo " Filtlong installer — macOS" echo "============================================================" echo echo "Conda environment: $ENV_NAME" echo "Git reference: $GIT_REF" echo if [[ ! "$ENV_NAME" =~ ^[A-Za-z0-9._-]+$ ]]; then echo "ERROR: Invalid Conda environment name:" echo " $ENV_NAME" echo echo "Use only letters, numbers, periods, underscores and hyphens." exit 1 fi if [ -z "$GIT_REF" ]; then echo "ERROR: The Git branch, tag or commit cannot be blank." exit 1 fi find_conda() { local candidate="" if [ -n "\${CONDA_EXE:-}" ] && [ -x "$CONDA_EXE" ]; then printf '%s\\n' "$CONDA_EXE" return 0 fi for candidate in \\ "$(command -v conda 2>/dev/null || true)" \\ "/opt/miniconda3/bin/conda" \\ "/opt/anaconda3/bin/conda" \\ "/opt/homebrew/Caskroom/miniconda/base/bin/conda" \\ "/opt/homebrew/Caskroom/miniforge/base/bin/conda" \\ "/usr/local/Caskroom/miniconda/base/bin/conda" \\ "/usr/local/Caskroom/miniforge/base/bin/conda" \\ "$HOME/miniconda3/bin/conda" \\ "$HOME/miniconda/bin/conda" \\ "$HOME/miniforge3/bin/conda" \\ "$HOME/mambaforge/bin/conda" \\ "$HOME/anaconda3/bin/conda" do if [ -n "$candidate" ] && [ -x "$candidate" ]; then printf '%s\\n' "$candidate" return 0 fi done return 1 } get_environment_prefix() { local prefix="" # First try to obtain the prefix from Python inside the environment. prefix="$( "$CONDA_BIN" run \\ -n "$ENV_NAME" \\ python -c 'import sys; print(sys.prefix)' \\ 2>/dev/null | tail -n 1 || true )" prefix="$( printf '%s' "$prefix" | tr -d '\\r' )" if [ -n "$prefix" ] && [ -d "$prefix" ]; then printf '%s\\n' "$prefix" return 0 fi # Fallback for an existing environment that does not contain Python. prefix="$( "$CONDA_BIN" env list 2>/dev/null | awk -v requested="$ENV_NAME" ' $1 == requested { print $NF exit } ' )" prefix="$( printf '%s' "$prefix" | tr -d '\\r' )" if [ -n "$prefix" ] && [ -d "$prefix" ]; then printf '%s\\n' "$prefix" return 0 fi return 1 } echo "Locating Conda..." CONDA_BIN="$(find_conda || true)" if [ -z "$CONDA_BIN" ]; then echo echo "ERROR: Conda was not found." echo echo "Install Miniconda or Miniforge, then run this installer again." exit 1 fi echo "Conda executable:" echo " $CONDA_BIN" CONDA_BASE="$( "$CONDA_BIN" info --base | tail -n 1 | tr -d '\\r' )" if [ -z "$CONDA_BASE" ] || [ ! -d "$CONDA_BASE" ]; then echo echo "ERROR: Could not determine the Conda base directory." exit 1 fi echo "Conda base:" echo " $CONDA_BASE" echo echo "Checking Conda environment: $ENV_NAME" if "$CONDA_BIN" run \\ -n "$ENV_NAME" \\ /usr/bin/true \\ >/dev/null 2>&1; then echo "Conda environment exists." else if [ "$CREATE_ENV" = "1" ]; then echo echo "Creating Conda environment: $ENV_NAME" "$CONDA_BIN" create \\ --yes \\ --name "$ENV_NAME" \\ --channel conda-forge \\ python=3.11 else echo echo "ERROR: Conda environment does not exist:" echo " $ENV_NAME" echo echo "Enable environment creation in the Observable controls," echo "or create the environment manually." exit 1 fi fi ENV_PREFIX="$( get_environment_prefix || true )" if [ -z "$ENV_PREFIX" ] || [ ! -d "$ENV_PREFIX" ]; then echo echo "ERROR: Could not determine the environment directory for:" echo " $ENV_NAME" echo echo "Available Conda environments:" "$CONDA_BIN" env list exit 1 fi echo echo "Environment directory:" echo " $ENV_PREFIX" # Install directly into the environment without running conda activate. DESTINATION="$ENV_PREFIX/bin/filtlong" mkdir -p "$ENV_PREFIX/bin" echo echo "Checking Apple Command Line Tools..." if ! command -v xcrun >/dev/null 2>&1 || ! xcrun --find clang++ >/dev/null 2>&1; then echo echo "ERROR: Apple Command Line Tools are required." echo echo "macOS may now open the Command Line Tools installer." echo "Complete that installation, then rerun this script." xcode-select --install >/dev/null 2>&1 || true exit 1 fi for required_command in git make clang++ install sed awk; do if ! command -v "$required_command" >/dev/null 2>&1; then echo echo "ERROR: Required command was not found:" echo " $required_command" echo echo "Install Apple Command Line Tools with:" echo " xcode-select --install" exit 1 fi done echo "Compiler:" echo " $(xcrun --find clang++)" echo "Make:" echo " $(command -v make)" echo "Git:" echo " $(command -v git)" if [ -x "$DESTINATION" ] && [ "$FORCE_REINSTALL" != "1" ]; then echo echo "Filtlong is already installed at:" echo " $DESTINATION" echo echo "No files were changed." echo echo "Enable replacement in the Observable controls to rebuild it." echo HELP_STATUS=0 HELP_OUTPUT="$( "$DESTINATION" -h 2>&1 )" || HELP_STATUS=$? printf '%s\\n' "$HELP_OUTPUT" | sed -n '1,8p' if [ "$HELP_STATUS" -gt 1 ]; then echo echo "WARNING: The existing executable returned status:" echo " $HELP_STATUS" fi exit 0 fi WORKDIR="$( mktemp -d "\${TMPDIR:-/tmp}/filtlong-build.XXXXXX" )" echo echo "Temporary build directory:" echo " $WORKDIR" cd "$WORKDIR" echo echo "Cloning Filtlong from GitHub..." git clone \\ --depth 1 \\ "$REPO_URL" \\ Filtlong cd Filtlong echo echo "Selecting Git reference: $GIT_REF" if git rev-parse \\ --verify \\ --quiet \\ "$GIT_REF^{commit}" \\ >/dev/null; then git checkout \\ --detach \\ "$GIT_REF" else echo "Fetching requested Git reference..." git fetch \\ --depth 1 \\ origin \\ "$GIT_REF" git checkout \\ --detach \\ FETCH_HEAD fi COMMIT="$( git rev-parse --short HEAD )" JOBS="$( sysctl -n hw.logicalcpu 2>/dev/null || printf '2' )" if ! [[ "$JOBS" =~ ^[0-9]+$ ]] || [ "$JOBS" -lt 1 ]; then JOBS=2 fi echo echo "Building Filtlong..." echo " Git commit: $COMMIT" echo " Parallel jobs: $JOBS" echo make \\ -j"$JOBS" \\ CXX=clang++ if [ ! -f "bin/filtlong" ]; then echo echo "ERROR: The build completed without producing:" echo " bin/filtlong" exit 1 fi if [ ! -x "bin/filtlong" ]; then chmod +x "bin/filtlong" fi echo echo "Installing Filtlong into the Conda environment..." echo " $DESTINATION" install \\ -m 755 \\ "bin/filtlong" \\ "$DESTINATION" if [ ! -x "$DESTINATION" ]; then echo echo "ERROR: The installed executable was not found or is not executable:" echo " $DESTINATION" exit 1 fi echo echo "Testing the installed executable..." HELP_STATUS=0 HELP_OUTPUT="$( "$DESTINATION" -h 2>&1 )" || HELP_STATUS=$? printf '%s\\n' "$HELP_OUTPUT" | sed -n '1,8p' if [ "$HELP_STATUS" -gt 1 ]; then echo echo "ERROR: The installed executable returned status:" echo " $HELP_STATUS" exit "$HELP_STATUS" fi echo echo "Confirming that Conda can locate Filtlong..." CONDA_VISIBLE_PATH="$( "$CONDA_BIN" run \\ -n "$ENV_NAME" \\ /usr/bin/which filtlong \\ 2>/dev/null | tail -n 1 || true )" CONDA_VISIBLE_PATH="$( printf '%s' "$CONDA_VISIBLE_PATH" | tr -d '\\r' )" if [ "$CONDA_VISIBLE_PATH" != "$DESTINATION" ]; then echo echo "WARNING: Filtlong was installed, but conda run returned:" echo " \${CONDA_VISIBLE_PATH:-not found}" echo echo "Expected:" echo " $DESTINATION" echo echo "The executable can still be run directly using the expected path." else echo "Conda located:" echo " $CONDA_VISIBLE_PATH" fi echo echo "============================================================" echo " Filtlong installed successfully" echo "============================================================" echo echo "Git commit:" echo " $COMMIT" echo echo "Conda environment:" echo " $ENV_NAME" echo echo "Executable:" echo " $DESTINATION" echo echo "Verify the installation at any time with:" echo echo " $CONDA_BIN run -n $ENV_NAME filtlong -h" echo echo "This installer did not use 'conda activate', so Conda shell" echo "activation and deactivation hooks were not executed." echo `; textarea.value = "bash <<'FILTLONG_INSTALLER'\n" + innerScript + "\nFILTLONG_INSTALLER"; status.textContent = ""; root.dispatchEvent( new Event("input", { bubbles: true }) ); } const controlsPanel = html`

Installer controls

${envInput} ${gitRefInput} ${createEnvInput} ${forceInput}

${copyBtn} ${openRepoBtn}

${status}

`; const scriptPanel = html`

Generated Mac script

${textarea}

`; const contentGrid = html`

${controlsPanel} ${scriptPanel}

`; const summary = html`

▶ Filtlong installer generator — macOS

`; const details = html`

${summary} ${contentGrid}

`; const note = html`

Copy the complete generated block and paste it directly into the macOS Terminal. Filtlong is installed directly inside the selected Conda environment without using conda activate, so Conda shell-hook errors are avoided. No sudo command is required.

`; const root = html`

${details} ${note}

`; details.addEventListener("toggle", () => { summary.textContent = details.open ? "▼ Filtlong installer generator — macOS" : "▶ Filtlong installer generator — macOS"; }); for (const control of [envInput, gitRefInput, createEnvInput, forceInput]) { control.addEventListener("input", generateScript); } copyBtn.addEventListener("click", async () => { try { await navigator.clipboard.writeText(textarea.value); status.textContent = "✅ Mac script copied to the clipboard."; } catch (error) { textarea.focus(); textarea.select(); const copied = document.execCommand("copy"); status.textContent = copied ? "✅ Mac script copied to the clipboard." : "⚠️ Copy failed. Select the script and copy it manually."; } }); openRepoBtn.addEventListener("click", () => { window.open( "https://github.com/rrwick/Filtlong", "_blank", "noopener,noreferrer" ); }); Object.defineProperty(root, "value", { get: () => textarea.value }); generateScript(); return root; }41:T52d9,viewof chopperLatestInstaller = { const envInput = Inputs.text({ label: "🧪 Conda environment name", value: "reads-assembly-core", style: "width: 100%;" }); const gitRefInput = Inputs.text({ label: "🌿 GitHub branch, tag, or commit", value: "master", placeholder: "master or a release tag", style: "width: 100%;" }); const createEnvInput = Inputs.toggle({ label: "➕ Create the Conda environment if missing", value: true }); const installBuildToolsInput = Inputs.toggle({ label: "🛠️ Install/update Rust and build tools", value: true }); const forceReinstallInput = Inputs.toggle({ label: "♻️ Recompile and replace existing Chopper", value: true }); const buttonStyle = ` padding: 0.5em 0.85em; border: 1px solid #bbb; border-radius: 6px; background: #f7f7f7; cursor: pointer; font-size: 0.9em; `; const textarea = html``; const copyBtn = html``; const githubBtn = html``; const status = html``; const arrow = html``; const title = html` Chopper installer generator — macOS `; const subtitle = html` Click to expand `; const summary = html`

`; summary.append(arrow, title, subtitle); const controlsHeading = html`

Installer controls

`; const controlsNote = html`

Update these settings to regenerate the Terminal installation script.

`; const controlsPanel = html`

`; controlsPanel.append( controlsHeading, controlsNote, envInput, gitRefInput, createEnvInput, installBuildToolsInput, forceReinstallInput ); const buttons = html`

`; buttons.append(copyBtn, githubBtn, status); const scriptHeading = html`

Generated Mac Terminal script

`; const scriptNote = html`

Copy the complete generated code and paste it directly into macOS Terminal. The installer avoids conda activate and adds the Conda library directory to Chopper's macOS runtime search path.

`; const scriptPanel = html`

`; scriptPanel.append(scriptHeading, buttons, textarea, scriptNote); const expandedContent = html`

`; expandedContent.append(controlsPanel, scriptPanel); const details = html`

`; details.append(summary, expandedContent); const scopedStyle = html``; const container = html`

`; container.append(scopedStyle, details); function shQuote(value) { return `'${String(value).replace(/'/g, `'\\''`)}'`; } function generateScript() { const envName = envInput.value.trim() || "reads-assembly-core"; const gitRef = gitRefInput.value.trim() || "master"; const createEnv = Boolean(createEnvInput.value); const installBuildTools = Boolean(installBuildToolsInput.value); const forceReinstall = Boolean(forceReinstallInput.value); const script = `bash <<'CHOPPER_INSTALLER' #!/usr/bin/env bash set -Eeuo pipefail ENV_NAME=${shQuote(envName)} GIT_REF=${shQuote(gitRef)} CREATE_ENV=${createEnv ? "1" : "0"} INSTALL_BUILD_TOOLS=${installBuildTools ? "1" : "0"} FORCE_REINSTALL=${forceReinstall ? "1" : "0"} REPO_URL="https://github.com/wdecoster/chopper.git" CONDA_EXE="" CONDA_BASE="" ENV_PREFIX="" ENV_LIB_DIR="" CHOPPER_BIN="" WORKDIR="" REPO_DIR="" SOURCE_COMMIT="" cleanup() { if [ -n "$WORKDIR" ] && [ -d "$WORKDIR" ]; then rm -rf "$WORKDIR" fi } on_error() { local status=$? trap - ERR echo echo "ERROR: Chopper installation failed at line $1." echo "Exit status: $status" echo echo "Review the messages above, correct the problem," echo "and run the installer again." exit "$status" } trap 'on_error "$LINENO"' ERR trap cleanup EXIT export PATH="/opt/homebrew/bin:/opt/homebrew/sbin:/usr/local/bin:/usr/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:$PATH" echo echo "============================================================" echo " Chopper installer — macOS" echo "============================================================" echo echo "Conda environment: $ENV_NAME" echo "GitHub reference: $GIT_REF" echo "Mac architecture: $(uname -m)" echo if [ "$(uname -s)" != "Darwin" ]; then echo "ERROR: This installer is intended for macOS." exit 1 fi if [[ ! "$ENV_NAME" =~ ^[A-Za-z0-9._-]+$ ]]; then echo "ERROR: Invalid Conda environment name:" echo " $ENV_NAME" echo echo "Use only letters, numbers, periods, underscores and hyphens." exit 1 fi if [ -z "$GIT_REF" ]; then echo "ERROR: The Git branch, tag or commit cannot be blank." exit 1 fi if ! xcode-select -p >/dev/null 2>&1; then echo "ERROR: Apple Command Line Tools are required." echo echo "macOS may now open the Command Line Tools installer." echo "Complete the installation, then run this script again." xcode-select --install >/dev/null 2>&1 || true exit 1 fi for mac_command in \\ /usr/bin/otool \\ /usr/bin/install_name_tool \\ /usr/bin/codesign; do if [ ! -x "$mac_command" ]; then echo "ERROR: Required macOS command was not found:" echo " $mac_command" exit 1 fi done find_conda() { local candidate="" if [ -n "\${CONDA_EXE:-}" ] && [ -x "$CONDA_EXE" ]; then printf '%s\\n' "$CONDA_EXE" return 0 fi for candidate in \\ "$(command -v conda 2>/dev/null || true)" \\ "/opt/miniconda3/bin/conda" \\ "/opt/anaconda3/bin/conda" \\ "/opt/homebrew/Caskroom/miniconda/base/bin/conda" \\ "/opt/homebrew/Caskroom/miniforge/base/bin/conda" \\ "/usr/local/Caskroom/miniconda/base/bin/conda" \\ "/usr/local/Caskroom/miniforge/base/bin/conda" \\ "$HOME/miniconda3/bin/conda" \\ "$HOME/miniconda/bin/conda" \\ "$HOME/miniforge3/bin/conda" \\ "$HOME/mambaforge/bin/conda" \\ "$HOME/anaconda3/bin/conda" do if [ -n "$candidate" ] && [ -x "$candidate" ]; then printf '%s\\n' "$candidate" return 0 fi done return 1 } get_environment_prefix() { local prefix="" prefix="$( "$CONDA_EXE" run \\ -n "$ENV_NAME" \\ python -c 'import sys; print(sys.prefix)' \\ 2>/dev/null | tail -n 1 || true )" prefix="$( printf '%s' "$prefix" | tr -d '\\r' )" if [ -n "$prefix" ] && [ -d "$prefix" ]; then printf '%s\\n' "$prefix" return 0 fi prefix="$( "$CONDA_EXE" env list 2>/dev/null | awk -v requested="$ENV_NAME" ' $1 == requested { print $NF exit } ' )" prefix="$( printf '%s' "$prefix" | tr -d '\\r' )" if [ -n "$prefix" ] && [ -d "$prefix" ]; then printf '%s\\n' "$prefix" return 0 fi return 1 } binary_has_rpath() { local binary="$1" local required_path="$2" /usr/bin/otool -l "$binary" | /usr/bin/awk ' $1 == "cmd" && $2 == "LC_RPATH" { reading_rpath = 1 next } reading_rpath == 1 && $1 == "path" { print $2 reading_rpath = 0 } ' | /usr/bin/grep -Fxq "$required_path" } repair_chopper_rpath() { local binary="$1" local library_directory="$2" if [ ! -x "$binary" ]; then echo echo "ERROR: Chopper executable was not found:" echo " $binary" return 1 fi if [ ! -d "$library_directory" ]; then echo echo "ERROR: Conda library directory was not found:" echo " $library_directory" return 1 fi echo echo "Checking Chopper's macOS runtime library path..." if binary_has_rpath \ "$binary" \ "$library_directory"; then echo "Required runtime path is already present:" echo " $library_directory" else echo "Adding Conda runtime library path:" echo " $library_directory" /usr/bin/install_name_tool \ -add_rpath "$library_directory" \ "$binary" fi echo "Applying an ad-hoc macOS code signature..." /usr/bin/codesign \ --force \ --sign - \ "$binary" if ! binary_has_rpath \ "$binary" \ "$library_directory"; then echo echo "ERROR: The required runtime path was not added:" echo " $library_directory" return 1 fi echo echo "Runtime library paths:" /usr/bin/otool -l "$binary" | /usr/bin/awk ' $1 == "cmd" && $2 == "LC_RPATH" { reading_rpath = 1 next } reading_rpath == 1 && $1 == "path" { print " " $2 reading_rpath = 0 } ' echo echo "Linked dynamic libraries:" /usr/bin/otool -L "$binary" } test_chopper() { echo echo "Testing Chopper directly..." "$CHOPPER_BIN" --version echo echo "Testing Chopper through Conda..." "$CONDA_EXE" run \\ --no-capture-output \\ -n "$ENV_NAME" \\ chopper --version } echo "Locating Conda..." CONDA_EXE="$(find_conda || true)" if [ -z "$CONDA_EXE" ]; then echo echo "ERROR: Conda was not found." echo echo "Install Miniconda or Miniforge, then run this installer again." exit 1 fi echo "Conda executable:" echo " $CONDA_EXE" CONDA_BASE="$( "$CONDA_EXE" info --base | tail -n 1 | tr -d '\\r' )" if [ -z "$CONDA_BASE" ] || [ ! -d "$CONDA_BASE" ]; then echo echo "ERROR: Could not determine the Conda base directory." exit 1 fi echo "Conda base:" echo " $CONDA_BASE" echo echo "Checking Conda environment: $ENV_NAME" if "$CONDA_EXE" run \\ -n "$ENV_NAME" \\ /usr/bin/true \\ >/dev/null 2>&1; then echo "Conda environment already exists." else if [ "$CREATE_ENV" = "1" ]; then echo echo "Creating Conda environment: $ENV_NAME" "$CONDA_EXE" create \\ --yes \\ --name "$ENV_NAME" \\ --channel conda-forge \\ python=3.11 else echo echo "ERROR: Conda environment does not exist:" echo " $ENV_NAME" echo echo "Enable environment creation in the Observable controls," echo "or create the environment manually." exit 1 fi fi ENV_PREFIX="$( get_environment_prefix || true )" if [ -z "$ENV_PREFIX" ] || [ ! -d "$ENV_PREFIX" ]; then echo echo "ERROR: Could not determine the environment directory for:" echo " $ENV_NAME" echo echo "Available Conda environments:" "$CONDA_EXE" env list exit 1 fi ENV_LIB_DIR="$ENV_PREFIX/lib" CHOPPER_BIN="$ENV_PREFIX/bin/chopper" echo echo "Environment directory:" echo " $ENV_PREFIX" echo "Environment library directory:" echo " $ENV_LIB_DIR" if [ "$INSTALL_BUILD_TOOLS" = "1" ]; then echo echo "Installing or updating Rust and build tools..." "$CONDA_EXE" install \\ --yes \\ --name "$ENV_NAME" \\ --channel conda-forge \\ rust \\ git \\ cmake \\ pkg-config \\ xz \\ bzip2 \\ zlib fi if [ ! -f "$ENV_LIB_DIR/liblzma.5.dylib" ]; then echo echo "ERROR: Conda's liblzma runtime library was not found:" echo " $ENV_LIB_DIR/liblzma.5.dylib" echo echo "Try rerunning with build-tool installation enabled." exit 1 fi echo echo "Checking build tools inside the Conda environment..." for required_command in git cargo rustc; do if ! "$CONDA_EXE" run \\ -n "$ENV_NAME" \\ "$required_command" \\ --version \\ >/dev/null 2>&1; then echo echo "ERROR: Required command is unavailable in $ENV_NAME:" echo " $required_command" echo echo "Enable build-tool installation in the Observable controls" echo "and run the installer again." exit 1 fi done echo echo "Build tools:" echo "Git:" "$CONDA_EXE" run \\ -n "$ENV_NAME" \\ git --version echo "Cargo:" "$CONDA_EXE" run \\ -n "$ENV_NAME" \\ cargo --version echo "Rust:" "$CONDA_EXE" run \\ -n "$ENV_NAME" \\ rustc --version if [ -x "$CHOPPER_BIN" ]; then echo echo "Existing Chopper executable found:" echo " $CHOPPER_BIN" repair_chopper_rpath \ "$CHOPPER_BIN" \ "$ENV_LIB_DIR" if [ "$FORCE_REINSTALL" != "1" ]; then echo echo "Force reinstall is disabled." echo "The existing executable was repaired and will now be tested." test_chopper echo echo "============================================================" echo " Existing Chopper installation is working" echo "============================================================" echo echo "Executable:" echo " $CHOPPER_BIN" exit 0 fi echo echo "Force reinstall is enabled." echo "Chopper will now be rebuilt and replaced." fi WORKDIR="$( mktemp -d "\${TMPDIR:-/tmp}/chopper-install.XXXXXX" )" REPO_DIR="$WORKDIR/chopper" echo echo "Temporary build directory:" echo " $WORKDIR" echo echo "Cloning Chopper from GitHub..." "$CONDA_EXE" run \\ --no-capture-output \\ -n "$ENV_NAME" \\ git clone \\ --filter=blob:none \\ "$REPO_URL" \\ "$REPO_DIR" echo echo "Fetching Git tags and branches..." "$CONDA_EXE" run \\ --no-capture-output \\ -n "$ENV_NAME" \\ git -C "$REPO_DIR" fetch \\ --tags \\ --force \\ origin echo echo "Selecting GitHub reference:" echo " $GIT_REF" if "$CONDA_EXE" run \\ -n "$ENV_NAME" \\ git -C "$REPO_DIR" rev-parse \\ --verify \\ --quiet "$GIT_REF^{commit}" \\ >/dev/null 2>&1; then CHECKOUT_REF="$GIT_REF" elif "$CONDA_EXE" run \\ -n "$ENV_NAME" \\ git -C "$REPO_DIR" rev-parse \\ --verify \\ --quiet "origin/$GIT_REF^{commit}" \\ >/dev/null 2>&1; then CHECKOUT_REF="origin/$GIT_REF" else echo "Fetching requested Git reference..." "$CONDA_EXE" run \\ --no-capture-output \\ -n "$ENV_NAME" \\ git -C "$REPO_DIR" fetch \\ --force \\ origin \\ "$GIT_REF" CHECKOUT_REF="FETCH_HEAD" fi "$CONDA_EXE" run \\ --no-capture-output \\ -n "$ENV_NAME" \\ git -C "$REPO_DIR" checkout \\ --detach \\ "$CHECKOUT_REF" SOURCE_COMMIT="$( "$CONDA_EXE" run \\ -n "$ENV_NAME" \\ git -C "$REPO_DIR" rev-parse --short HEAD | tail -n 1 | tr -d '\\r' )" echo echo "Source commit:" echo " $SOURCE_COMMIT" CARGO_ARGS=( install --path "$REPO_DIR" --root "$ENV_PREFIX" ) if [ -f "$REPO_DIR/Cargo.lock" ]; then CARGO_ARGS+=(--locked) fi if [ "$FORCE_REINSTALL" = "1" ]; then CARGO_ARGS+=(--force) fi echo echo "Compiling and installing Chopper..." echo echo "Embedding this runtime library path during linking:" echo " $ENV_LIB_DIR" echo "$CONDA_EXE" run \\ --no-capture-output \\ -n "$ENV_NAME" \\ /usr/bin/env \\ "RUSTFLAGS=-C link-arg=-Wl,-rpath,$ENV_LIB_DIR" \\ cargo "\${CARGO_ARGS[@]}" if [ ! -x "$CHOPPER_BIN" ]; then echo echo "ERROR: Installation completed without creating:" echo " $CHOPPER_BIN" exit 1 fi repair_chopper_rpath \ "$CHOPPER_BIN" \ "$ENV_LIB_DIR" test_chopper CONDA_VISIBLE_PATH="$( "$CONDA_EXE" run \\ -n "$ENV_NAME" \\ /usr/bin/which chopper \\ 2>/dev/null | tail -n 1 | tr -d '\\r' || true )" if [ "$CONDA_VISIBLE_PATH" != "$CHOPPER_BIN" ]; then echo echo "WARNING: Chopper was installed, but conda run returned:" echo " \${CONDA_VISIBLE_PATH:-not found}" echo echo "Expected:" echo " $CHOPPER_BIN" else echo echo "Conda located Chopper at:" echo " $CONDA_VISIBLE_PATH" fi echo echo "============================================================" echo " Chopper installation completed successfully" echo "============================================================" echo echo "Git commit:" echo " $SOURCE_COMMIT" echo echo "Conda environment:" echo " $ENV_NAME" echo echo "Executable:" echo " $CHOPPER_BIN" echo echo "Runtime library directory:" echo " $ENV_LIB_DIR" echo echo "Verify the installation later with:" echo echo " $CONDA_EXE run -n $ENV_NAME chopper --version" echo echo "Run Chopper without activating Conda with:" echo echo " $CONDA_EXE run --no-capture-output -n $ENV_NAME chopper --help" echo echo "This installer did not use 'conda activate'." CHOPPER_INSTALLER`; textarea.value = script; status.textContent = ""; container.dispatchEvent( new Event("input", { bubbles: true }) ); } for (const control of [ envInput, gitRefInput, createEnvInput, installBuildToolsInput, forceReinstallInput ]) { control.addEventListener("input", generateScript); } details.addEventListener("toggle", () => { const isOpen = details.open; arrow.textContent = isOpen ? "▼" : "▶"; subtitle.textContent = isOpen ? "Click to collapse" : "Click to expand"; }); copyBtn.addEventListener("click", async () => { try { await navigator.clipboard.writeText(textarea.value); status.textContent = "✅ Copied"; } catch (error) { textarea.focus(); textarea.select(); const copied = document.execCommand("copy"); status.textContent = copied ? "✅ Copied" : "❌ Copy failed — select the code manually"; } }); githubBtn.addEventListener("click", () => { window.open( "https://github.com/wdecoster/chopper", "_blank", "noopener,noreferrer" ); }); Object.defineProperty(container, "value", { get: () => textarea.value }); generateScript(); return container; }42:T2acf,viewof excelSupportToolsMacInstaller = { const envInput = Inputs.text({ label: "🧪 Conda environment name", value: "reads-assembly-core", style: "width: 100%; box-sizing: border-box;" }); const installPandasInput = Inputs.toggle({ label: "Install pandas", value: true }); const installOpenpyxlInput = Inputs.toggle({ label: "Install openpyxl (.xlsx reading and writing)", value: true }); const installXlsxwriterInput = Inputs.toggle({ label: "Install XlsxWriter (formatted Excel exports)", value: true }); const installXlrdInput = Inputs.toggle({ label: "Install xlrd (older .xls file reading)", value: false }); const installXlwtInput = Inputs.toggle({ label: "Install xlwt (older .xls file writing)", value: false }); const installPyarrowInput = Inputs.toggle({ label: "Install pyarrow (optional fast table processing)", value: false }); const upgradeInput = Inputs.toggle({ label: "Upgrade packages if already installed", value: true }); const verifyInput = Inputs.toggle({ label: "Run installation verification", value: true }); const textarea = html` `; const copyBtn = html` `; function shellQuote(value) { return `'${String(value).replace(/'/g, `'\\''`)}'`; } function generateScript() { const envName = envInput.value.trim() || "reads-assembly-core"; const packages = []; if (installPandasInput.value) { packages.push("pandas"); } if (installOpenpyxlInput.value) { packages.push("openpyxl"); } if (installXlsxwriterInput.value) { packages.push("xlsxwriter"); } if (installXlrdInput.value) { packages.push("xlrd"); } if (installXlwtInput.value) { packages.push("xlwt"); } if (installPyarrowInput.value) { packages.push("pyarrow"); } const packageString = packages.length > 0 ? packages.map(shellQuote).join(" ") : ""; const pipInstallCommand = upgradeInput.value ? `"$CONDA_EXE" run -n "$ENV_NAME" python -m pip install --upgrade ${packageString}` : `"$CONDA_EXE" run -n "$ENV_NAME" python -m pip install ${packageString}`; const verificationImports = []; if (installPandasInput.value) { verificationImports.push(` import pandas print("✅ pandas:", pandas.__version__)`); } if (installOpenpyxlInput.value) { verificationImports.push(` import openpyxl print("✅ openpyxl:", openpyxl.__version__)`); } if (installXlsxwriterInput.value) { verificationImports.push(` import xlsxwriter print("✅ XlsxWriter:", xlsxwriter.__version__)`); } if (installXlrdInput.value) { verificationImports.push(` import xlrd print("✅ xlrd:", xlrd.__version__)`); } if (installXlwtInput.value) { verificationImports.push(` import xlwt print("✅ xlwt imported successfully")`); } if (installPyarrowInput.value) { verificationImports.push(` import pyarrow print("✅ pyarrow:", pyarrow.__version__)`); } const verificationSection = verifyInput.value && verificationImports.length > 0 ? ` echo echo "🔍 Verifying installed Excel-support tools..." VERIFY_FILE="/tmp/excel_support_verify_$$.py" cat > "$VERIFY_FILE" <<'PYTHON_VERIFY' ${verificationImports.join("\n")} print() print("✅ All selected Excel-support tools imported successfully.") PYTHON_VERIFY "$CONDA_EXE" run -n "$ENV_NAME" \ python "$VERIFY_FILE" 2>&1 | tee -a "$LOG_FILE" rm -f "$VERIFY_FILE" ` : ""; const noPackagesSelected = packages.length === 0 ? ` echo "⚠️ No Excel-support packages were selected." echo "Nothing was installed." exit 0 ` : ""; const innerScript = `set -Eeuo pipefail ENV_NAME=${shellQuote(envName)} LOG_FILE="$HOME/excel_support_tools_mac_install.log" trap 'STATUS=$?; echo; echo "Installation failed at line $LINENO with exit code $STATUS." | tee -a "$LOG_FILE"; exit "$STATUS"' ERR echo "============================================================" echo "📊 Excel Support Tools Installer for macOS" echo "============================================================" echo "Environment: $ENV_NAME" echo "Log file: $LOG_FILE" echo { echo "Excel-support installation started: $(date)" echo "Environment: $ENV_NAME" echo } > "$LOG_FILE" ${noPackagesSelected} # Add common Homebrew and Conda locations to PATH. export PATH="/opt/homebrew/bin:/usr/local/bin:$HOME/miniconda3/bin:$HOME/anaconda3/bin:/opt/miniconda3/bin:/opt/anaconda3/bin:$PATH" echo "🔎 Locating Conda..." CONDA_EXE="" if command -v conda >/dev/null 2>&1; then CONDA_EXE="$(command -v conda)" elif [ -x "/opt/miniconda3/bin/conda" ]; then CONDA_EXE="/opt/miniconda3/bin/conda" elif [ -x "$HOME/miniconda3/bin/conda" ]; then CONDA_EXE="$HOME/miniconda3/bin/conda" elif [ -x "/opt/anaconda3/bin/conda" ]; then CONDA_EXE="/opt/anaconda3/bin/conda" elif [ -x "$HOME/anaconda3/bin/conda" ]; then CONDA_EXE="$HOME/anaconda3/bin/conda" else echo "Conda was not found." echo echo "Install Miniconda first, then run this installer again." echo echo "Common expected locations:" echo " /opt/miniconda3" echo " $HOME/miniconda3" echo " /opt/anaconda3" echo " $HOME/anaconda3" exit 1 fi echo "✅ Conda found: $CONDA_EXE" | tee -a "$LOG_FILE" CONDA_BASE="$("$CONDA_EXE" info --base)" echo "✅ Conda base: $CONDA_BASE" | tee -a "$LOG_FILE" echo echo "🔎 Checking for Conda environment: $ENV_NAME" if "$CONDA_EXE" env list | awk '{print $1}' | grep -Fxq "$ENV_NAME" then echo "✅ Environment already exists: $ENV_NAME" | tee -a "$LOG_FILE" else echo "📦 Environment does not exist." echo "📦 Creating $ENV_NAME with a current compatible Python version..." "$CONDA_EXE" create \ --name "$ENV_NAME" \ python \ pip \ --yes 2>&1 | tee -a "$LOG_FILE" fi echo echo "🐍 Checking the Python installation..." "$CONDA_EXE" run -n "$ENV_NAME" \ python --version 2>&1 | tee -a "$LOG_FILE" "$CONDA_EXE" run -n "$ENV_NAME" \ python -c "import sys; print('Python executable:', sys.executable)" \ 2>&1 | tee -a "$LOG_FILE" echo echo "⬆️ Updating pip, setuptools, and wheel..." "$CONDA_EXE" run -n "$ENV_NAME" \ python -m pip install \ --upgrade \ pip \ setuptools \ wheel 2>&1 | tee -a "$LOG_FILE" echo echo "📊 Installing selected Excel-support packages..." ${pipInstallCommand} 2>&1 | tee -a "$LOG_FILE" ${verificationSection} echo echo "============================================================" echo "✅ Excel-support tools installation complete" echo "============================================================" echo echo "Environment:" echo " $ENV_NAME" echo echo "Python version used:" "$CONDA_EXE" run -n "$ENV_NAME" python --version echo echo "Activate the environment later with:" echo " conda activate $ENV_NAME" echo echo "Installation log:" echo " $LOG_FILE" echo echo "Press Enter to close..." read -r _ /dev/null || true bash -s <<'EXCEL_SUPPORT_INSTALLER' ${innerScript} EXCEL_SUPPORT_INSTALLER`; } function updateScript() { textarea.value = generateScript(); } const controls = [ envInput, installPandasInput, installOpenpyxlInput, installXlsxwriterInput, installXlrdInput, installXlwtInput, installPyarrowInput, upgradeInput, verifyInput ]; for (const control of controls) { control.addEventListener("input", updateScript); control.addEventListener("change", updateScript); } copyBtn.onclick = async () => { try { await navigator.clipboard.writeText(textarea.value); copyBtn.textContent = "✅ Copied!"; setTimeout(() => { copyBtn.textContent = "📋 Copy Mac Installation Script"; }, 2000); } catch (error) { textarea.focus(); textarea.select(); document.execCommand("copy"); copyBtn.textContent = "✅ Copied!"; setTimeout(() => { copyBtn.textContent = "📋 Copy Mac Installation Script"; }, 2000); } }; updateScript(); return html`

📊 Install Excel Support Tools on macOS ▸

Installation controls

${controls}

Generated Mac installation script

${textarea}

${copyBtn}

`; }43:T2bfe,viewof medakaLatestInstaller = { const envInput = Inputs.text({ label: "🧪 Conda environment name", value: "reads-assembly-core", placeholder: "reads-assembly-core", style: "width: 320px" }); const pythonInput = Inputs.select(["3.10", "3.11", "3.12", "3.13"], { label: "🐍 Python version for a new environment", value: "3.11", style: "width: 180px" }); const allowUpdatesInput = Inputs.toggle({ label: "🔄 Allow Conda to update environment dependencies", value: true }); const textarea = html``; const buttonStyle = ` padding: 0.55em 0.9em; border: 1px solid #b8b8b8; border-radius: 6px; background: #f7f7f7; cursor: pointer; font-size: 0.9em; `; const copyBtn = html``; const githubBtn = html``; const status = html``; function shQuote(value) { return `'${String(value).replace(/'/g, `'\\''`)}'`; } function generateScript() { const envName = String(envInput.value ?? "").trim() || "reads-assembly-core"; const pythonVersion = String(pythonInput.value ?? "").trim() || "3.11"; const allowUpdates = Boolean(allowUpdatesInput.value); const innerScript = `#!/usr/bin/env bash set -Eeuo pipefail trap 'status=$?; echo; echo "❌ Medaka installation failed at line $LINENO (exit $status)."; exit $status' ERR ENV_NAME=${shQuote(envName)} PYTHON_VERSION=${shQuote(pythonVersion)} ALLOW_DEPENDENCY_UPDATES=${allowUpdates ? "true" : "false"} echo echo "============================================================" echo " Medaka installer for macOS" echo "============================================================" echo echo "Conda environment : $ENV_NAME" echo "New-env Python : $PYTHON_VERSION" echo "Mac architecture : $(uname -m)" echo if [ "$(uname -s)" != "Darwin" ]; then echo "❌ This installer is intended for macOS." echo " Detected operating system: $(uname -s)" exit 1 fi if [[ ! "$ENV_NAME" =~ ^[A-Za-z0-9._-]+$ ]]; then echo "❌ Invalid Conda environment name: $ENV_NAME" echo " Use only letters, numbers, periods, underscores, and hyphens." exit 1 fi case "$PYTHON_VERSION" in 3.10|3.11|3.12|3.13) ;; *) echo "❌ Medaka requires Python 3.10 through Python 3.13." exit 1 ;; esac find_conda() { if command -v conda >/dev/null 2>&1; then command -v conda return 0 fi for candidate in \\ /opt/miniconda3/bin/conda \\ /opt/anaconda3/bin/conda \\ /usr/local/miniconda3/bin/conda \\ /usr/local/anaconda3/bin/conda \\ "$HOME/miniconda3/bin/conda" \\ "$HOME/anaconda3/bin/conda" \\ "$HOME/miniforge3/bin/conda" \\ "$HOME/mambaforge/bin/conda" do if [ -x "$candidate" ]; then printf '%s\\n' "$candidate" return 0 fi done return 1 } CONDA_EXE="$(find_conda)" || { echo "❌ Conda could not be found." echo echo "Expected locations include:" echo " /opt/miniconda3/bin/conda" echo " $HOME/miniconda3/bin/conda" echo " $HOME/miniforge3/bin/conda" echo echo "Install Miniconda or Miniforge, then run this installer again." exit 1 } echo "✅ Conda found:" echo " $CONDA_EXE" echo eval "$("$CONDA_EXE" shell.bash hook)" echo "Conda version:" conda --version echo ENV_EXISTS=false if conda env list | awk 'NF && $1 !~ /^#/ {print $1}' | grep -Fxq "$ENV_NAME" then ENV_EXISTS=true fi if [ "$ENV_EXISTS" = "true" ]; then echo "✅ Existing Conda environment found: $ENV_NAME" ENV_PYTHON="$( conda run -n "$ENV_NAME" python -c \\ 'import sys; print(f"{sys.version_info.major}.{sys.version_info.minor}")' \\ 2>/dev/null || true )" if [ -z "$ENV_PYTHON" ]; then echo "❌ Python could not be run in environment: $ENV_NAME" exit 1 fi echo " Current Python version: $ENV_PYTHON" case "$ENV_PYTHON" in 3.10|3.11|3.12|3.13) ;; *) echo echo "❌ The existing environment uses Python $ENV_PYTHON." echo " Current Medaka versions require Python 3.10–3.13." echo echo "Use another environment name or update Python in this environment." exit 1 ;; esac else echo "Environment '$ENV_NAME' does not exist." echo "Creating it with Python $PYTHON_VERSION..." echo conda create -y \\ -n "$ENV_NAME" \\ -c conda-forge \\ "python=$PYTHON_VERSION" \\ pip fi echo echo "Preparing installation options..." if [ "$ALLOW_DEPENDENCY_UPDATES" = "true" ]; then CONDA_BEHAVIOUR="--update-deps" echo "Conda may update dependencies when required." else CONDA_BEHAVIOUR="--freeze-installed" echo "Conda will try to preserve currently installed dependencies." fi echo echo "Installing Medaka from the official nanoporetech Conda channel..." echo INSTALL_METHOD="" if conda install -y $CONDA_BEHAVIOUR \\ -n "$ENV_NAME" \\ -c conda-forge \\ -c nanoporetech \\ -c bioconda \\ medaka then INSTALL_METHOD="Official nanoporetech Conda package" else echo echo "⚠️ The official Conda installation was unsuccessful." echo "Trying the official PyPI installation instead..." echo conda install -y $CONDA_BEHAVIOUR \\ -n "$ENV_NAME" \\ -c conda-forge \\ -c bioconda \\ pip \\ "samtools>=1.14" \\ "minimap2>=2.17" \\ htslib conda run -n "$ENV_NAME" \\ python -m pip install --upgrade pip setuptools wheel conda run -n "$ENV_NAME" \\ python -m pip install --upgrade medaka INSTALL_METHOD="Official PyPI package" fi echo echo "============================================================" echo " Verifying Medaka installation" echo "============================================================" echo MEDAKA_VERSION="$( conda run -n "$ENV_NAME" \\ python -c 'import medaka; print(medaka.__version__)' )" echo "Medaka version:" echo " $MEDAKA_VERSION" echo echo "Medaka command:" conda run -n "$ENV_NAME" medaka --help >/dev/null echo " ✅ medaka" echo echo "Medaka consensus command:" conda run -n "$ENV_NAME" medaka_consensus --help >/dev/null echo " ✅ medaka_consensus" echo echo "Samtools version:" conda run -n "$ENV_NAME" samtools --version | head -n 1 echo echo "Minimap2 version:" conda run -n "$ENV_NAME" minimap2 --version echo echo "Checking bgzip and tabix..." conda run -n "$ENV_NAME" bash -lc \\ 'command -v bgzip >/dev/null && command -v tabix >/dev/null' echo " ✅ bgzip" echo " ✅ tabix" echo echo "============================================================" echo " ✅ Medaka installation completed" echo "============================================================" echo echo "Installation method:" echo " $INSTALL_METHOD" echo echo "Environment:" echo " $ENV_NAME" echo echo "To activate the environment later, run:" echo echo " conda activate $ENV_NAME" echo echo "To confirm the installed version, run:" echo echo " medaka --version" echo echo "To list available polishing models, run:" echo echo " medaka tools list_models" echo echo "A basic polishing command is:" echo echo " medaka_consensus -i reads.fastq.gz -d assembly.fasta -o medaka_output -t 8" echo `; return `bash <<'MEDAKA_INSTALLER' ${innerScript} MEDAKA_INSTALLER`; } const panel = html`

🧬 Medaka installer generator — macOS

${envInput} ${pythonInput}

${allowUpdatesInput}

The generated script installs Medaka into the selected Conda environment. It first tries the official nanoporetech Conda package and automatically falls back to the official PyPI package if necessary. Required command-line tools such as samtools, minimap2, bgzip, and tabix are also checked.

${copyBtn} ${githubBtn} ${status}

${textarea}

`; function updateScript() { const script = generateScript(); textarea.value = script; panel.value = script; panel.dispatchEvent( new Event("input", { bubbles: true }) ); } envInput.addEventListener("input", updateScript); pythonInput.addEventListener("input", updateScript); allowUpdatesInput.addEventListener("input", updateScript); copyBtn.addEventListener("click", async () => { const script = textarea.value; try { await navigator.clipboard.writeText(script); status.textContent = "✅ Copied"; status.style.color = "#237a32"; } catch (error) { textarea.focus(); textarea.select(); const copied = document.execCommand("copy"); if (copied) { status.textContent = "✅ Copied"; status.style.color = "#237a32"; } else { status.textContent = "❌ Copy failed"; status.style.color = "#a32020"; } } setTimeout(() => { status.textContent = ""; }, 2500); }); githubBtn.addEventListener("click", () => { window.open( "https://github.com/nanoporetech/medaka", "_blank", "noopener,noreferrer" ); }); updateScript(); return panel; }44:[] 2c:{"id":"c1c861aacd3ea50e","slug":"mac-script","title":"Nanopore Sequencing Scripts for Mac","thumbnail":"17792310103c1e65d65891c2beb6e70981f2cb333cc7bfa7020004b6d3a709e2","access_level":"public","create_time":"$D2026-07-17T17:59:08.206Z","update_time":"$D2026-07-23T20:01:17.215Z","view_time":null,"first_public_time":"$D2026-07-17T18:20:30.996Z","has_unpublished_edits":null,"fork":false,"stars":0,"starred":false,"owner":{"type":"team","id":"d1dfc5f860fb8699","login":"phage","name":"WabushOnce","avatar_url":"https://avatars-next.observableusercontent.com/9303f26b98fd8f7e04b66a6ac3218bfd2ca7e146f15ba24ca32ffac15f802763","tier":"starter_2024"},"version":185,"publish_version":null,"role":null,"authored":false,"authors":[{"type":"individual","id":"3035ce62f81ebcd9","login":"phage","name":"WabushOnce","avatar_url":"https://avatars-next.observableusercontent.com/9303f26b98fd8f7e04b66a6ac3218bfd2ca7e146f15ba24ca32ffac15f802763","tier":null}],"members":[{"type":"individual","id":"3035ce62f81ebcd9","login":"phage","name":"WabushOnce","avatar_url":"https://avatars-next.observableusercontent.com/9303f26b98fd8f7e04b66a6ac3218bfd2ca7e146f15ba24ca32ffac15f802763","tier":null,"role":"editor"},{"type":"team","id":"d1dfc5f860fb8699","login":"phage","name":"WabushOnce","avatar_url":"https://avatars-next.observableusercontent.com/9303f26b98fd8f7e04b66a6ac3218bfd2ca7e146f15ba24ca32ffac15f802763","tier":"starter_2024","role":"editor"}],"comments":[],"custom_thumbnail":true,"trashed":false,"lapsed":null,"subscribed":null,"forks":1,"collection":null,"type":"notebook","body":{"title":"Nanopore Sequencing Scripts for Mac","cells":[{"id":41,"value":"$2e","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":45,"value":"DoradoVersion = md`## 📦 Dorado - Check for the latest version\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":31,"value":"$2f","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":15,"value":"$30","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":48,"value":"Dorado = md`\n---\n## 📦 Dorado - Basecalling via WSL\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":9,"value":"$31","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":59,"value":"Merge_Barcodes = md`\n---\n## 📦 Merge Multiple FastQ Files \n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":53,"value":"$32","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":129,"value":"Remove_Host = md`\n---\n## 📦 Remove Bacterial Reads\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":126,"value":"$33","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":56,"value":"NanoComp = md`\n---\n## 📦 Create NanoComp Files\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":77,"value":"$34","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":95,"value":"Filter_Filtlong = md`\n---\n## 📦 Filter Reads\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":92,"value":"$35","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":100,"value":"$36","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":88,"value":"Flye = md`\n---\n## 📦 Genome Assembly with Flye\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":71,"value":"$37","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":82,"value":"$38","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":182,"value":"$39","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":176,"value":"Create_BAM = md`\n---\n## 📦 View Read Coverage\n- Create .BAM Files\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":173,"value":"$3a","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":165,"value":"PharokkaAnnotation = md`\n---\n## 📦 Genome Annotation with Pharokka\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":163,"value":"$3b","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":170,"value":"$3c","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":160,"value":"BatchRename = md`\n---\n## 📦 Batch Rename Files and Folders\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":157,"value":"$3d","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":105,"value":"Installers = md`\n---\n## 📦 Program Installation Scripts\n\n`","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":152,"value":"---","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"","database":"$undefined"},{"id":64,"value":"$3e","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":74,"value":"$3f","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":103,"value":"$40","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":116,"value":"$41","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":134,"value":"$42","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":112,"value":"$43","pinned":false,"hidden":false,"mode":"ojs","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W44","stdlib":"1","titling":"auto"}} 2d:"$2c:body"