28:null 29:["$","title",null,{"children":"Installation Scripts for Tools to Assemble and Evaluate Nanopore Sequences | WabushOnce | Observable"}] 2e:T408,viewof wslInstallGuide = { const container = html`

🧰 Install WSL on Windows (click to expand)

To run Dorado and other Linux-based tools on Windows, you’ll first need to install WSL (Windows Subsystem for Linux).

Install WSL
Windows Start Menu, find & run PowerShell as Administrator, then run the following code:
```
wsl --install
```
Then restart your computer.
Install a Linux Distribution (e.g., Ubuntu)
After restarting, run WSL from the Start menu:

`; return container; }2f:T7c5,viewof resetWslPassword = { const powershellScript = `# Launch Windows PowerShell as Administrator # List WSL distributions: wsl -l -v # Launch distro as root (replace 'Ubuntu' if needed): wsl -d Ubuntu -u root`; const wslScript = `# Inside WSL (as root) # Change the password for your WSL user: passwd your-username # Replace 'your-username' with your actual username # Exit WSL: exit # Back in PowerShell, set your user as the default: ubuntu config --default-user your-username`; const pwText = Inputs.textarea({ value: powershellScript, rows: 6, style: "width: 100%; font-family: monospace;" }); const wslText = Inputs.textarea({ value: wslScript, rows: 9, style: "width: 100%; font-family: monospace;" }); const copyBtn1 = html``; copyBtn1.onclick = () => { navigator.clipboard.writeText(pwText.value); copyBtn1.textContent = "✅ Copied!"; setTimeout( () => (copyBtn1.textContent = "📋 Copy PowerShell Script"), 1500 ); }; const copyBtn2 = html``; copyBtn2.onclick = () => { navigator.clipboard.writeText(wslText.value); copyBtn2.textContent = "✅ Copied!"; setTimeout(() => (copyBtn2.textContent = "📋 Copy WSL Script"), 1500); }; const container = html`

🔐 Don't know the Admin Password? Reset password.

💡 Step 1: Launch Windows PowerShell as Administrator, then copy and run this:

${pwText} ${copyBtn1}

💡 Step 2: Inside the WSL terminal (as root), run the following:

${wslText} ${copyBtn2}

`; return container; }30:T5d9,viewof doradoBinaryInstaller = { const script = `#!/bin/bash # 🧬 Dorado v1.0.2 Precompiled Binary Installer for WSL # 📁 Step 1: Create a folder for Dorado rm -rf ~/Dorado # ⬇️ Step 2: Download precompiled Dorado release wget https://cdn.oxfordnanoportal.com/software/analysis/dorado-1.0.2-linux-x64.tar.gz # 📦 Step 3: Extract the archive tar -xvzf dorado-1.0.2-linux-x64.tar.gz # 🛠️ Step 4: Add Dorado to your PATH echo 'export PATH="$HOME/dorado-1.0.2-linux-x64/bin:$PATH"' >> ~/.bashrc source ~/.bashrc # 🧪 Step 5: Test Dorado dorado --version `; const textarea = Inputs.textarea({ value: script, rows: script.split("\n").length + 2, style: "width: 100%; font-family: monospace;" }); const copyButton = html``; copyButton.onclick = () => { navigator.clipboard.writeText(script); copyButton.textContent = "✅ Copied!"; setTimeout( () => (copyButton.textContent = "📋 Copy Dorado Installer"), 1500 ); }; return html`

⬇️ Install Precompiled Dorado from GitHub

Paste this script into your WSL terminal to install and configure Dorado.

${textarea} ${copyButton}

`; }31:T43f4,viewof installCoreNanoporeToolsWSL = { const installScript = `bash <<'CORE_NANOPORE_INSTALLER' #!/usr/bin/env bash # ============================================================ # Core Nanopore Tools Installer — WSL # # Conda environment: # reads-assembly-core # # Installs with Conda: # Flye # Racon # Filtlong # NanoPlot # Samtools # BCFtools # HTSlib / Tabix / bgzip # Minimap2 # pyabpoa # pandas # openpyxl # XlsxWriter # # Installs from official PyPI package: # Medaka # # Dorado is intentionally not installed. # ============================================================ set -Eeuo pipefail ENV_NAME="reads-assembly-core" PYTHON_VERSION="3.12" LOG_FILE="$HOME/reads_assembly_core_install.log" MINIFORGE_DIR="$HOME/miniforge3" TEMP_INSTALLER="" # ------------------------------------------------------------ # Cleanup # ------------------------------------------------------------ cleanup() { if [ -n "\${TEMP_INSTALLER:-}" ] && [ -f "\${TEMP_INSTALLER:-}" ]; then rm -f "$TEMP_INSTALLER" fi } trap cleanup EXIT # ------------------------------------------------------------ # Error reporting # ------------------------------------------------------------ trap ' status=$? echo echo "============================================================" echo "❌ Core Nanopore tools installation failed" echo "============================================================" echo echo "Failed near script line:" echo " $LINENO" echo echo "Exit code:" echo " $status" echo echo "Installation log:" echo " $LOG_FILE" echo exit "$status" ' ERR # Start a new log. : > "$LOG_FILE" # Display and log all subsequent output. exec > >(tee -a "$LOG_FILE") 2>&1 echo echo "============================================================" echo " Core Nanopore Tools Installer — WSL" echo "============================================================" echo echo "Installation started:" echo " $(date)" echo echo "Environment:" echo " $ENV_NAME" echo echo "Requested Python:" echo " $PYTHON_VERSION" echo echo "Installation log:" echo " $LOG_FILE" echo # ------------------------------------------------------------ # Confirm Linux / WSL # ------------------------------------------------------------ if [ "$(uname -s)" != "Linux" ]; then echo "❌ ERROR: This installer must run in WSL or Linux." exit 1 fi if grep -qi microsoft /proc/version 2>/dev/null; then echo "✅ WSL detected." else echo "ℹ️ Linux detected." echo " WSL was not explicitly detected." fi echo # ------------------------------------------------------------ # Locate Conda # ------------------------------------------------------------ find_conda() { local candidate="" if command -v conda >/dev/null 2>&1; then command -v conda return 0 fi for candidate in \ "$HOME/miniforge3/bin/conda" \ "$HOME/miniconda3/bin/conda" \ "$HOME/miniconda/bin/conda" \ "$HOME/anaconda3/bin/conda" do if [ -x "$candidate" ]; then printf '%s\\n' "$candidate" return 0 fi done return 1 } CONDA_EXE="$(find_conda || true)" # ------------------------------------------------------------ # Install Miniforge if Conda is unavailable # ------------------------------------------------------------ if [ -z "$CONDA_EXE" ]; then echo "ℹ️ Conda was not found." echo echo "📦 Installing Miniforge in:" echo " $MINIFORGE_DIR" echo if [ -e "$MINIFORGE_DIR" ]; then echo "❌ ERROR: This directory already exists:" echo " $MINIFORGE_DIR" echo echo "However, a working Conda executable was not found there." echo "The directory may contain an incomplete installation." exit 1 fi case "$(uname -m)" in x86_64|amd64) MINIFORGE_ARCH="x86_64" ;; aarch64|arm64) MINIFORGE_ARCH="aarch64" ;; *) echo "❌ ERROR: Unsupported processor architecture:" echo " $(uname -m)" exit 1 ;; esac MINIFORGE_URL="https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-$MINIFORGE_ARCH.sh" TEMP_INSTALLER="$(mktemp -t miniforge-installer.XXXXXX.sh)" echo "⬇️ Downloading Miniforge..." if command -v curl >/dev/null 2>&1; then curl \ --fail \ --location \ --retry 3 \ --output "$TEMP_INSTALLER" \ "$MINIFORGE_URL" elif command -v wget >/dev/null 2>&1; then wget \ --tries=3 \ --output-document="$TEMP_INSTALLER" \ "$MINIFORGE_URL" else echo "❌ ERROR: Neither curl nor wget is available." exit 1 fi if [ ! -s "$TEMP_INSTALLER" ]; then echo "❌ ERROR: The Miniforge installer was not downloaded." exit 1 fi echo echo "📦 Installing Miniforge..." bash "$TEMP_INSTALLER" \ -b \ -p "$MINIFORGE_DIR" CONDA_EXE="$MINIFORGE_DIR/bin/conda" fi # ------------------------------------------------------------ # Verify and initialize Conda # ------------------------------------------------------------ if [ ! -x "$CONDA_EXE" ]; then echo "❌ ERROR: Conda executable was not found:" echo " $CONDA_EXE" exit 1 fi CONDA_BASE="$("$CONDA_EXE" info --base)" echo "✅ Conda found." echo echo "Conda executable:" echo " $CONDA_EXE" echo echo "Conda base:" echo " $CONDA_BASE" echo echo "Conda version:" "$CONDA_EXE" --version echo CONDA_SH="$CONDA_BASE/etc/profile.d/conda.sh" if [ ! -f "$CONDA_SH" ]; then echo "❌ ERROR: Conda initialization file was not found:" echo " $CONDA_SH" exit 1 fi set +u source "$CONDA_SH" set -u # Configure future Bash terminals. "$CONDA_EXE" init bash >/dev/null 2>&1 || true # ------------------------------------------------------------ # Channel configuration # # nanoporetech is intentionally excluded from Conda package # resolution. Medaka will be installed from its official PyPI # binary package after the Conda environment is complete. # # --override-channels prevents any existing defaults entry in # ~/.condarc from being used. # ------------------------------------------------------------ CHANNEL_ARGS=( --override-channels --strict-channel-priority --channel conda-forge --channel bioconda ) echo "📡 Conda channels:" echo " 1. conda-forge" echo " 2. bioconda" echo echo "The following channels will not be used:" echo " - defaults" echo " - nanoporetech" echo # ------------------------------------------------------------ # Detect the environment # ------------------------------------------------------------ environment_exists() { "$CONDA_EXE" env list | awk 'NF && $1 !~ /^#/ {print $1}' | grep -Fxq "$ENV_NAME" } if environment_exists; then echo "♻️ Existing environment detected:" echo " $ENV_NAME" echo echo "Updating its Python and package-management tools..." echo "$CONDA_EXE" install \ --name "$ENV_NAME" \ --yes \ "\${CHANNEL_ARGS[@]}" \ "python=$PYTHON_VERSION" \ pip \ setuptools \ wheel else echo "🆕 Creating environment:" echo " $ENV_NAME" echo "$CONDA_EXE" create \ --name "$ENV_NAME" \ --yes \ "\${CHANNEL_ARGS[@]}" \ "python=$PYTHON_VERSION" \ pip \ setuptools \ wheel fi # ------------------------------------------------------------ # Install assembly and read-analysis tools # ------------------------------------------------------------ echo echo "============================================================" echo "Installing assembly and read-analysis tools" echo "============================================================" echo "$CONDA_EXE" install \ --name "$ENV_NAME" \ --yes \ "\${CHANNEL_ARGS[@]}" \ flye \ racon \ filtlong \ nanoplot # ------------------------------------------------------------ # Install alignment and sequence-file tools # ------------------------------------------------------------ echo echo "============================================================" echo "Installing alignment and sequence-file tools" echo "============================================================" echo "$CONDA_EXE" install \ --name "$ENV_NAME" \ --yes \ "\${CHANNEL_ARGS[@]}" \ samtools \ bcftools \ htslib \ minimap2 # htslib supplies tabix and bgzip. # ------------------------------------------------------------ # Install Python and Excel-support tools # ------------------------------------------------------------ echo echo "============================================================" echo "Installing Python and Excel-support tools" echo "============================================================" echo "$CONDA_EXE" install \ --name "$ENV_NAME" \ --yes \ "\${CHANNEL_ARGS[@]}" \ pandas \ openpyxl \ xlsxwriter \ pyabpoa # ------------------------------------------------------------ # Activate environment # ------------------------------------------------------------ echo echo "🐍 Activating $ENV_NAME..." set +u conda activate "$ENV_NAME" set -u hash -r ACTIVE_ENV="\${CONDA_DEFAULT_ENV:-}" if [ "$ACTIVE_ENV" != "$ENV_NAME" ]; then echo "❌ ERROR: The expected environment was not activated." echo echo "Expected:" echo " $ENV_NAME" echo echo "Active:" echo " $ACTIVE_ENV" exit 1 fi echo "✅ Environment activated." echo echo "Python executable:" echo " $(command -v python)" echo echo "Python version:" python --version echo # ------------------------------------------------------------ # Install official Medaka PyPI package # ------------------------------------------------------------ echo echo "============================================================" echo "Installing Medaka from the official PyPI package" echo "============================================================" echo python -m pip install \ --upgrade \ pip \ setuptools \ wheel python -m pip install \ --upgrade \ --prefer-binary \ medaka echo echo "Checking Python package dependencies..." python -m pip check # ------------------------------------------------------------ # Command verification # ------------------------------------------------------------ echo echo "============================================================" echo "Verifying command-line programs" echo "============================================================" echo FAILED_COMMANDS=() check_command() { local label="$1" local command_name="$2" local command_path="" command_path="$(command -v "$command_name" || true)" if [ -n "$command_path" ]; then echo "✅ $label" echo " $command_path" else echo "❌ $label was not found." FAILED_COMMANDS+=("$label") fi } check_command "Flye" "flye" check_command "Racon" "racon" check_command "Filtlong" "filtlong" check_command "NanoPlot" "NanoPlot" check_command "Samtools" "samtools" check_command "BCFtools" "bcftools" check_command "HTSlib Tabix" "tabix" check_command "HTSlib bgzip" "bgzip" check_command "Minimap2" "minimap2" check_command "Medaka" "medaka" check_command "Medaka consensus" "medaka_consensus" # ------------------------------------------------------------ # Version verification # ------------------------------------------------------------ echo echo "============================================================" echo "Installed versions" echo "============================================================" echo echo "--- Python ---" python --version echo echo "--- Flye ---" flye --version echo echo "--- Racon ---" racon --version echo echo "--- Filtlong ---" filtlong --version echo echo "--- NanoPlot ---" NanoPlot --version echo echo "--- Samtools ---" samtools --version echo echo "--- BCFtools ---" bcftools --version echo echo "--- Tabix ---" tabix --version echo echo "--- bgzip ---" bgzip --version echo echo "--- Minimap2 ---" minimap2 --version echo echo "--- Medaka ---" medaka --version echo # ------------------------------------------------------------ # Python import verification # ------------------------------------------------------------ echo echo "============================================================" echo "Verifying Python packages" echo "============================================================" echo PYTHON_VERIFY_FAILED=0 if ! python - <<'PYTHON_VERIFY' import importlib import importlib.metadata packages = [ ("pandas", "pandas"), ("openpyxl", "openpyxl"), ("XlsxWriter", "xlsxwriter"), ("pyabpoa", "pyabpoa"), ("medaka", "medaka"), ] failures = [] for distribution_name, module_name in packages: try: importlib.import_module(module_name) try: version = importlib.metadata.version(distribution_name) except importlib.metadata.PackageNotFoundError: version = "version unavailable" print(f"✅ {distribution_name}: {version}") except Exception as error: failures.append(distribution_name) print( f"❌ {distribution_name}: " f"{type(error).__name__}: {error}" ) if failures: print() print("Failed Python imports:") for package in failures: print(f" - {package}") raise SystemExit(1) print() print("✅ All requested Python imports passed.") PYTHON_VERIFY then PYTHON_VERIFY_FAILED=1 fi # ------------------------------------------------------------ # Final result # ------------------------------------------------------------ echo if [ "\${#FAILED_COMMANDS[@]}" -gt 0 ] || [ "$PYTHON_VERIFY_FAILED" -ne 0 ]; then echo "============================================================" echo "❌ Installation verification failed" echo "============================================================" echo if [ "\${#FAILED_COMMANDS[@]}" -gt 0 ]; then echo "Missing command-line programs:" for program in "\${FAILED_COMMANDS[@]}"; do echo " - $program" done echo fi echo "Review the installation log:" echo " $LOG_FILE" echo exit 1 fi echo "============================================================" echo "✅ Core Nanopore tools installation complete" echo "============================================================" echo echo "Environment:" echo " $ENV_NAME" echo echo "To activate it in a new WSL terminal:" echo echo " conda activate $ENV_NAME" echo echo "Then verify selected programs with:" echo echo " flye --version" echo " racon --version" echo " filtlong --version" echo " NanoPlot --version" echo " samtools --version" echo " bcftools --version" echo " minimap2 --version" echo " medaka --version" echo echo "Dorado is not installed by this script." echo echo "Installation log:" echo " $LOG_FILE" echo echo "Installation completed:" echo " $(date)" echo exit 0 CORE_NANOPORE_INSTALLER `; const textarea = Inputs.textarea({ value: installScript, rows: 68, style: ` width: 100%; min-height: 900px; box-sizing: border-box; font-family: ui-monospace, SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace; font-size: 0.88rem; line-height: 1.35; white-space: pre; resize: vertical; ` }); textarea.readOnly = true; const copyBtn = html` `; const status = html` `; copyBtn.onclick = async () => { try { await navigator.clipboard.writeText(installScript); copyBtn.textContent = "✅ Copied!"; status.textContent = "Paste the complete script into a WSL terminal."; status.style.color = "#16723a"; setTimeout(() => { copyBtn.textContent = "📋 Copy WSL Installation Script"; status.textContent = ""; }, 2500); } catch (error) { status.textContent = "Copy failed. Select the script and copy it manually."; status.style.color = "#a12622"; } }; return html`

🧬 Install Core Nanopore Tools in WSL — Flye, Racon, Filtlong, NanoPlot, Medaka, Samtools, BCFtools, Minimap2 and Excel support

This installer uses Python 3.12, installs core tools from conda-forge and bioconda, and installs the official Medaka binary using pip. It avoids both the Anaconda defaults channel and the Conda package conflict encountered previously.

${textarea}

${copyBtn} ${status}

`; }32:T1d1b,viewof installNanoCompWSL = { const installScript = `bash <<'NANOCOMP_INSTALL_SCRIPT' #!/usr/bin/env bash # 🧬 Install NanoComp in reads-assembly-core under WSL # # This version installs directly into the requested Conda environment. # It does not rely on "conda activate", so the package cannot accidentally # be installed into the base environment. set -uo pipefail ENV_NAME="reads-assembly-core" LOG_FILE="$HOME/install_nanocomp_reads_assembly_core.log" # Start a fresh log for this installation attempt. : > "$LOG_FILE" # Log all subsequent output while still displaying it in the terminal. exec > >(tee -a "$LOG_FILE") 2>&1 pause_and_exit() { local status="$1" echo echo "📄 Installation log:" echo " $LOG_FILE" echo echo "Press Enter to exit..." read -r _ || true exit "$status" } echo "============================================================" echo " NanoComp installer for WSL" echo "============================================================" echo echo "Installation started: $(date)" echo "Target environment: $ENV_NAME" echo # Add common system and Conda locations to PATH. export PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$HOME/miniconda/bin:$HOME/miniconda3/bin:$HOME/anaconda3/bin:$PATH" hash -r # Confirm that Conda is available. if ! command -v conda >/dev/null 2>&1; then echo "❌ ERROR: Conda was not found." echo echo "Open WSL and confirm that this command works:" echo echo " conda --version" echo pause_and_exit 1 fi echo "✅ Conda found:" echo " $(command -v conda)" echo # Find the exact filesystem location of the requested environment. ENV_PREFIX="$( conda env list | awk -v target="$ENV_NAME" ' $1 == target { print $NF exit } ' )" if [ -z "$ENV_PREFIX" ]; then echo "❌ ERROR: Conda environment '$ENV_NAME' was not found." echo echo "Available Conda environments:" conda env list echo pause_and_exit 1 fi PYTHON_BIN="$ENV_PREFIX/bin/python" NANOCOMP_BIN="$ENV_PREFIX/bin/NanoComp" echo "✅ Target environment found:" echo " $ENV_PREFIX" echo if [ ! -x "$PYTHON_BIN" ]; then echo "❌ ERROR: Python was not found in the target environment." echo echo "Expected Python executable:" echo " $PYTHON_BIN" echo pause_and_exit 1 fi echo "Target Python:" echo " $PYTHON_BIN" "$PYTHON_BIN" --version echo # Check specifically inside reads-assembly-core. # Do not use plain 'command -v NanoComp' here because that could detect # the copy that was previously installed in the base environment. if [ -x "$NANOCOMP_BIN" ]; then echo "🔍 NanoComp is already present in $ENV_NAME." echo if "$NANOCOMP_BIN" --version; then echo echo "✅ NanoComp is already installed correctly." echo echo "NanoComp executable:" echo " $NANOCOMP_BIN" echo echo "To use NanoComp:" echo " conda activate $ENV_NAME" echo " NanoComp --version" echo pause_and_exit 0 fi echo echo "⚠️ The existing NanoComp executable did not run correctly." echo " The installer will reinstall it." echo fi echo "============================================================" echo "Trying installation with Conda" echo "============================================================" echo echo "Channels:" echo " 1. conda-forge" echo " 2. bioconda" echo echo "Installing directly into:" echo " $ENV_PREFIX" echo # --override-channels prevents the defaults channels from being used. # -p installs into the exact target environment path. if conda install \ -y \ -p "$ENV_PREFIX" \ --override-channels \ -c conda-forge \ -c bioconda \ nanocomp then echo echo "✅ Conda installation command completed." else echo echo "⚠️ Conda could not solve the installation." echo " The installer will try pip using the target environment's" echo " exact Python executable." fi echo echo "🔍 Checking NanoComp inside $ENV_NAME..." if [ -x "$NANOCOMP_BIN" ] && "$NANOCOMP_BIN" --version; then echo echo "✅ NanoComp was installed successfully with Conda." else echo echo "============================================================" echo "Trying installation with pip" echo "============================================================" echo echo "Pip will run through this exact Python executable:" echo " $PYTHON_BIN" echo # Make sure pip exists inside the target environment. if ! "$PYTHON_BIN" -m pip --version >/dev/null 2>&1; then echo "⚠️ Pip was not found in $ENV_NAME." echo " Attempting to add pip with Python ensurepip..." echo if ! "$PYTHON_BIN" -m ensurepip --upgrade; then echo echo "❌ ERROR: Could not add pip to $ENV_NAME." pause_and_exit 1 fi fi echo "Pip location:" "$PYTHON_BIN" -m pip --version echo if ! "$PYTHON_BIN" -m pip install --upgrade NanoComp; then echo echo "❌ ERROR: Pip installation failed." pause_and_exit 1 fi fi echo echo "============================================================" echo "Final verification" echo "============================================================" echo if [ ! -x "$NANOCOMP_BIN" ]; then echo "❌ ERROR: NanoComp was not found in the target environment." echo echo "Expected executable:" echo " $NANOCOMP_BIN" echo pause_and_exit 1 fi if ! "$NANOCOMP_BIN" --version; then echo echo "❌ ERROR: NanoComp is present but did not run successfully." pause_and_exit 1 fi echo echo "✅ NanoComp installation completed successfully." echo echo "Environment:" echo " $ENV_NAME" echo echo "Environment directory:" echo " $ENV_PREFIX" echo echo "Python executable:" echo " $PYTHON_BIN" echo echo "NanoComp executable:" echo " $NANOCOMP_BIN" echo echo "To use NanoComp later:" echo echo " conda activate $ENV_NAME" echo " which python" echo " which NanoComp" echo " NanoComp --version" echo pause_and_exit 0 NANOCOMP_INSTALL_SCRIPT `; const textarea = Inputs.textarea({ value: installScript, rows: 62, style: "width: 100%; font-family: monospace; white-space: pre;" }); const copyBtn = html` `; copyBtn.onclick = async () => { try { await navigator.clipboard.writeText(installScript); copyBtn.textContent = "✅ Copied!"; } catch (error) { copyBtn.textContent = "❌ Copy failed"; console.error(error); } setTimeout(() => { copyBtn.textContent = "📋 Copy NanoComp Install Script"; }, 2000); }; return html`

🧬 Install NanoComp in reads-assembly-core (WSL — exact environment installation)

${textarea}

${copyBtn}

`; }33:T2915,viewof installQuastWSL = { const installScript = `bash <<'QUAST_INSTALLER' #!/usr/bin/env bash # 🧬 Install QUAST in WSL # Target environment: reads-assembly-core set -Eeuo pipefail ENV_NAME="reads-assembly-core" TARGET_PYTHON="3.12" QUAST_VERSION="5.3.0" LOG_FILE="$HOME/install_quast_reads_assembly_core.log" pause_before_exit() { echo read -r -p "Press Enter to exit..." _ "$LOG_FILE" exec > >(tee -a "$LOG_FILE") 2>&1 echo "============================================================" echo " QUAST installer for WSL" echo "============================================================" echo echo "Environment: $ENV_NAME" echo "Target Python: $TARGET_PYTHON" echo "QUAST version: $QUAST_VERSION" echo "Started: $(date)" echo "Log file: $LOG_FILE" echo # ------------------------------------------------------------ # 1. Find Conda # ------------------------------------------------------------ export PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$PATH" hash -r if ! command -v conda >/dev/null 2>&1; then echo "🔍 Conda is not currently on PATH." echo " Checking common installation locations..." echo for CONDA_CANDIDATE in \\ "$HOME/miniconda/bin/conda" \\ "$HOME/miniconda3/bin/conda" \\ "$HOME/anaconda3/bin/conda" \\ "/opt/miniconda3/bin/conda" \\ "/opt/conda/bin/conda" do if [ -x "$CONDA_CANDIDATE" ]; then export PATH="$(dirname "$CONDA_CANDIDATE"):$PATH" hash -r break fi done fi if ! command -v conda >/dev/null 2>&1; then die "Conda could not be found." fi echo "✅ Conda found:" echo " $(command -v conda)" echo # Initialize Conda for this Bash process. eval "$(conda shell.bash hook)" # Ensure that no previously activated environment affects installation. conda deactivate >/dev/null 2>&1 || true echo "Conda version:" conda --version echo # ------------------------------------------------------------ # 2. Confirm that the target environment exists # ------------------------------------------------------------ echo "🔍 Checking environment: $ENV_NAME" if ! conda run -n "$ENV_NAME" python -c \\ 'import sys; print(sys.executable)' >/dev/null 2>&1 then die "The '$ENV_NAME' environment was not found or does not contain Python." fi ENV_PREFIX_BEFORE="$(conda run -n "$ENV_NAME" python -c \\ 'import os; print(os.environ["CONDA_PREFIX"])')" PYTHON_PATH_BEFORE="$(conda run -n "$ENV_NAME" python -c \\ 'import sys; print(sys.executable)')" PY_VER_BEFORE="$(conda run -n "$ENV_NAME" python -c \\ 'import sys; print(str(sys.version_info.major) + "." + str(sys.version_info.minor))')" echo "✅ Environment found." echo " Prefix: $ENV_PREFIX_BEFORE" echo " Python: $PYTHON_PATH_BEFORE" echo " Python version: $PY_VER_BEFORE" echo # ------------------------------------------------------------ # 3. Install QUAST into reads-assembly-core # ------------------------------------------------------------ echo "📦 Preparing QUAST installation..." echo echo "Channels:" echo " 1. conda-forge" echo " 2. bioconda" echo echo "The defaults channel will not be used." echo CONDA_INSTALL_HELP="$(conda install --help 2>&1 || true)" if [ "$PY_VER_BEFORE" = "3.14" ]; then echo "⚠️ Python 3.14 is not compatible with the available" echo " Bioconda QUAST packages." echo echo "The environment will be changed to Python $TARGET_PYTHON." echo "Python and QUAST will be solved in the same Conda transaction." echo if [[ "$CONDA_INSTALL_HELP" == *"--no-pin"* ]]; then conda install \\ --no-pin \\ -n "$ENV_NAME" \\ -y \\ --override-channels \\ -c conda-forge \\ -c bioconda \\ "python=$TARGET_PYTHON" \\ "quast=$QUAST_VERSION" else conda install \\ -n "$ENV_NAME" \\ -y \\ --override-channels \\ -c conda-forge \\ -c bioconda \\ "python=$TARGET_PYTHON" \\ "quast=$QUAST_VERSION" fi else echo "✅ Python $PY_VER_BEFORE does not require the Python 3.14 correction." echo conda install \\ -n "$ENV_NAME" \\ -y \\ --override-channels \\ -c conda-forge \\ -c bioconda \\ "quast=$QUAST_VERSION" fi echo echo "✅ Conda package transaction completed." echo # ------------------------------------------------------------ # 4. Refresh and verify the target environment # ------------------------------------------------------------ hash -r ENV_PREFIX="$(conda run -n "$ENV_NAME" python -c \\ 'import os; print(os.environ["CONDA_PREFIX"])')" PYTHON_PATH="$(conda run -n "$ENV_NAME" python -c \\ 'import sys; print(sys.executable)')" PY_VER="$(conda run -n "$ENV_NAME" python -c \\ 'import sys; print(str(sys.version_info.major) + "." + str(sys.version_info.minor))')" QUAST_EXE="$ENV_PREFIX/bin/quast.py" echo "🔍 Verifying the completed installation..." echo echo "Environment prefix:" echo " $ENV_PREFIX" echo echo "Python executable:" echo " $PYTHON_PATH" echo echo "Python version:" echo " $PY_VER" echo echo "Expected QUAST executable:" echo " $QUAST_EXE" echo if [ ! -x "$QUAST_EXE" ]; then die "QUAST was not found inside '$ENV_NAME' after installation." fi case "$QUAST_EXE" in "$ENV_PREFIX"/*) echo "✅ QUAST belongs to the correct Conda environment." ;; *) die "The detected QUAST executable is outside '$ENV_NAME'." ;; esac echo echo "Installed Conda package:" conda list -n "$ENV_NAME" quast # ------------------------------------------------------------ # 5. Run QUAST smoke tests # ------------------------------------------------------------ echo echo "🧪 Testing the QUAST version command..." echo QUAST_VERSION_OUTPUT="$("$QUAST_EXE" --version 2>&1 || true)" echo "$QUAST_VERSION_OUTPUT" if echo "$QUAST_VERSION_OUTPUT" | grep -q "QUAST v"; then echo echo "✅ QUAST version command completed successfully." else die "QUAST is installed, but the version command did not run correctly." fi echo echo "🧪 Testing the QUAST help command..." echo QUAST_HELP_FILE="$(mktemp)" if "$QUAST_EXE" --help >"$QUAST_HELP_FILE" 2>&1; then if grep -qi "usage" "$QUAST_HELP_FILE" || grep -qi "quast" "$QUAST_HELP_FILE" then echo "✅ QUAST help loaded successfully." else cat "$QUAST_HELP_FILE" rm -f "$QUAST_HELP_FILE" die "The QUAST help command ran but did not produce the expected output." fi else cat "$QUAST_HELP_FILE" rm -f "$QUAST_HELP_FILE" die "QUAST is installed, but the help command failed." fi rm -f "$QUAST_HELP_FILE" # ------------------------------------------------------------ # 6. Final report # ------------------------------------------------------------ echo echo "============================================================" echo "✅ QUAST installation complete" echo "============================================================" echo echo "Environment:" echo " $ENV_NAME" echo echo "Environment prefix:" echo " $ENV_PREFIX" echo echo "Python version:" echo " $PY_VER" echo echo "QUAST executable:" echo " $QUAST_EXE" echo echo "QUAST version:" "$QUAST_EXE" --version echo echo "To use QUAST later:" echo echo " conda activate $ENV_NAME" echo " hash -r" echo " which quast.py" echo " quast.py --version" echo " quast.py --help" echo echo "Example:" echo echo " quast.py assembly.fasta -o quast_results" echo echo "Installation log:" echo " $LOG_FILE" echo echo "Optional QUAST downloads:" echo echo " quast-download-gridss" echo " quast-download-silva" echo " quast-download-busco" echo echo "These optional downloads are not required for standard" echo "phage genome assembly assessment." echo echo "Note:" echo " A previous pip-installed copy of QUAST may still exist in" echo " the base environment. Activate $ENV_NAME before running" echo " QUAST so that this Conda installation is used." echo pause_before_exit QUAST_INSTALLER `; const textarea = Inputs.textarea({ value: installScript, rows: 52, style: ` width: 100%; min-height: 780px; box-sizing: border-box; font-family: ui-monospace, SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace; font-size: 13px; line-height: 1.4; white-space: pre; ` }); const copyBtn = html``; copyBtn.onclick = async () => { try { await navigator.clipboard.writeText(installScript); copyBtn.textContent = "✅ Copied!"; setTimeout(() => { copyBtn.textContent = "📋 Copy QUAST Install Script"; }, 2000); } catch (error) { copyBtn.textContent = "❌ Copy failed"; setTimeout(() => { copyBtn.textContent = "📋 Copy QUAST Install Script"; }, 2000); console.error("Could not copy QUAST installer:", error); } }; return html`

🧬 Install QUAST in reads-assembly-core (WSL)

Installs QUAST 5.3.0 into the reads-assembly-core Conda environment. Python 3.14 is changed to Python 3.12 when necessary. The installation is verified using the QUAST version and help commands.

${textarea}

${copyBtn}

`; }34:T1706,viewof mummerInstallGenerator = { const condaEnvName = Inputs.text({ label: "Conda environment name", value: "reads-assembly-core", style: "width: 320px" }); const textarea = html``; const copyBtn = html``; copyBtn.onclick = () => { navigator.clipboard.writeText(textarea.value); copyBtn.textContent = "Copied!"; setTimeout(() => (copyBtn.textContent = "Copy"), 1200); }; function bashEscape(s) { return String(s || "").replace(/"/g, '\\"'); } function updateScript() { const envName = (condaEnvName.value || "").trim(); const lines = [ "#!/bin/bash", "# Install MUMmer in WSL for a conda environment", "", "set -u", "set -o pipefail", "", 'export PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:$PATH"', "hash -r", "", 'LOG_FILE="$HOME/install_mummer_reads_assembly_core.log"', `ENV_NAME="${bashEscape(envName)}"`, "", 'echo "📝 Logging to $LOG_FILE"', 'echo "MUMmer installation started at $(date)" > "$LOG_FILE"', 'echo "PATH=$PATH" | tee -a "$LOG_FILE"', "", "if ! command -v conda >/dev/null 2>&1; then", ' echo "❌ ERROR: conda not found in this shell." | tee -a "$LOG_FILE"', ' echo "Open WSL and ensure conda works first." | tee -a "$LOG_FILE"', " exit 1", "fi", "", "# Initialize conda for this shell", 'eval "$(conda shell.bash hook)" 2>>"$LOG_FILE" || {', ' echo "❌ ERROR: failed to initialize conda in this shell." | tee -a "$LOG_FILE"', " exit 1", "}", "", "conda deactivate >/dev/null 2>&1 || true", "", `if ! conda env list | awk '{print $1}' | grep -Fx "${bashEscape( envName )}" >/dev/null 2>&1; then`, ` echo "❌ ERROR: '${bashEscape( envName )}' environment not found." | tee -a "$LOG_FILE"`, ' echo "Create it first before installing MUMmer." | tee -a "$LOG_FILE"', " exit 1", "fi", "", 'echo "📜 Accepting Anaconda Terms of Service..." | tee -a "$LOG_FILE"', 'conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/main >>"$LOG_FILE" 2>&1 || true', 'conda tos accept --override-channels --channel https://repo.anaconda.com/pkgs/r >>"$LOG_FILE" 2>&1 || true', "", 'echo "🔧 Setting channels..." | tee -a "$LOG_FILE"', 'conda config --add channels defaults >>"$LOG_FILE" 2>&1 || true', 'conda config --add channels bioconda >>"$LOG_FILE" 2>&1 || true', 'conda config --add channels conda-forge >>"$LOG_FILE" 2>&1 || true', "", 'echo "🐍 Activating $ENV_NAME..." | tee -a "$LOG_FILE"', 'conda activate "$ENV_NAME" >>"$LOG_FILE" 2>&1 || {', ' echo "❌ ERROR: failed to activate $ENV_NAME" | tee -a "$LOG_FILE"', " exit 1", "}", "", "hash -r", "", 'echo "📦 Installing MUMmer via conda..." | tee -a "$LOG_FILE"', 'conda install -n "$ENV_NAME" -y mummer 2>&1 | tee -a "$LOG_FILE"', 'INSTALL_EXIT="${PIPESTATUS[0]}"', "", 'if [ "$INSTALL_EXIT" -ne 0 ]; then', ' echo "❌ ERROR: conda install returned exit code $INSTALL_EXIT" | tee -a "$LOG_FILE"', " exit 1", "fi", "", 'conda deactivate >>"$LOG_FILE" 2>&1 || true', 'conda activate "$ENV_NAME" >>"$LOG_FILE" 2>&1 || {', ' echo "❌ ERROR: failed to reactivate $ENV_NAME after install" | tee -a "$LOG_FILE"', " exit 1", "}", "", "hash -r", "", 'echo "🔍 Verifying installation..." | tee -a "$LOG_FILE"', "", 'NUCMER_PATH="$(command -v nucmer || true)"', 'MUMMERPLOT_PATH="$(command -v mummerplot || true)"', "", 'if [ -n "$NUCMER_PATH" ]; then', ' echo "✅ nucmer found at: $NUCMER_PATH" | tee -a "$LOG_FILE"', "else", ' echo "❌ nucmer not found in PATH after installation." | tee -a "$LOG_FILE"', "fi", "", 'if [ -n "$MUMMERPLOT_PATH" ]; then', ' echo "✅ mummerplot found at: $MUMMERPLOT_PATH" | tee -a "$LOG_FILE"', "else", ' echo "❌ mummerplot not found in PATH after installation." | tee -a "$LOG_FILE"', "fi", "", 'if [ -n "$NUCMER_PATH" ]; then', ' echo "nucmer --help output:" | tee -a "$LOG_FILE"', ' nucmer --help >>"$LOG_FILE" 2>&1 || true', "fi", "", 'if [ -n "$NUCMER_PATH" ]; then', ' echo "✅ MUMmer installed successfully!" | tee -a "$LOG_FILE"', ' echo "👉 To use MUMmer:" | tee -a "$LOG_FILE"', ' echo "conda activate $ENV_NAME" | tee -a "$LOG_FILE"', ' echo "nucmer --help" | tee -a "$LOG_FILE"', ' echo "mummerplot --help" | tee -a "$LOG_FILE"', ' echo "📄 Log saved to: $LOG_FILE" | tee -a "$LOG_FILE"', " exit 0", "else", ' echo "❌ ERROR: MUMmer installation verification failed." | tee -a "$LOG_FILE"', ' echo "📄 Log saved to: $LOG_FILE" | tee -a "$LOG_FILE"', " exit 1", "fi" ]; textarea.value = lines.join("\n"); } [condaEnvName].forEach((input) => input.addEventListener("input", updateScript) ); updateScript(); return html`

Generate WSL script to install MUMmer
Copy the generated bash into a .sh file, then run it in WSL with bash filename.sh.

${condaEnvName}

${copyBtn}

${textarea}

`; }35:T923,viewof checkInstalledNanoporeTools = { const checkScript = `#!/bin/bash # 📋 Check installed versions of common Nanopore tools in reads-assembly-core # Save as check_nanopore_tools.sh and run with: bash check_nanopore_tools.sh output_file="nanopore_tools_versions.txt" echo "🔍 Checking tool versions..." > "$output_file" # 📦 Activate conda environment if [[ -f "$HOME/miniconda/etc/profile.d/conda.sh" ]]; then source "$HOME/miniconda/etc/profile.d/conda.sh" conda activate reads-assembly-core else echo "⚠️ Conda not found. Skipping environment activation." >> "$output_file" fi # Check CLI tools for tool in dorado flye racon medaka chopper filtlong NanoPlot minimap2; do if command -v "$tool" &> /dev/null; then echo "$tool: $($tool --version 2>&1 | head -n 1)" >> "$output_file" else echo "$tool: ❌ NOT FOUND" >> "$output_file" fi done # Check Python Excel support libraries echo -e "\\n🔎 Checking Excel support libraries (Python)..." >> "$output_file" for mod in pandas openpyxl xlsxwriter; do python -c "import $mod; print('$mod: ✅ Found (v' + $mod.__version__ + ')')" 2>> "$output_file" >> "$output_file" || echo "$mod: ❌ NOT FOUND" >> "$output_file" done # Final output abs_path=$(realpath "$output_file") echo "✅ Done. Output saved to $abs_path" cat "$output_file"`; const textarea = Inputs.textarea({ value: checkScript, rows: checkScript.split("\n").length + 2, style: "width: 100%; font-family: monospace;" }); const copyButton = html``; copyButton.onclick = () => { navigator.clipboard.writeText(checkScript); copyButton.textContent = "✅ Copied"; setTimeout(() => (copyButton.textContent = "📋 Copy Script"), 1500); }; return html`

🩺 Verify all Tools are Installed (click to expand)

💡 This script checks tool versions inside the reads-assembly-core conda environment and saves the output to nanopore_tools_versions.txt. Run it in WSL.

${textarea} ${copyButton}

`; }36:T573,viewof threadHelper = { const bashCmd = `# 🧠 Check CPU Thread Count nproc`; const recommendationText = `💡 Recommendation: Use approximately 75% of your threads for tools like medaka_consensus. For example, if 'nproc' returns 8, use -t 6.`; const text1 = Inputs.textarea({ value: bashCmd, rows: 3, style: "width: 100%; font-family: monospace;" }); const copyBtn1 = html``; copyBtn1.onclick = () => { navigator.clipboard.writeText(bashCmd); copyBtn1.textContent = "✅ Copied!"; setTimeout(() => (copyBtn1.textContent = "📋 Copy 'nproc' Command"), 2000); }; const recommendationMarkup = html`

${recommendationText}

`; return html`

🧵 Check Threads & Get Threading Advice

🔧 Paste the following in your WSL terminal to see how many CPU threads are available:

${text1} ${copyBtn1}

💬 Then use this guidance to set thread count for tools like Medaka:

${recommendationMarkup}

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