28:null 29:["$","title",null,{"children":"Phage Bioinformatics Software Installer | WabushOnce | Observable"}] 2e:T1008,display(html`

Before running the installer

The selected bioinformatics programs run using WSL (Windows Subsystem for Linux). WSL allows Linux programs to run directly on a Windows 11 computer.

If WSL is not already installed:

Open PowerShell as Administrator.
Enter:
```
wsl --install
```
Restart the computer if Windows asks you to.
After restarting, open WSL from the Windows Start menu.
The first time WSL opens, it may complete its setup and ask you to create a Linux username and password.
When a command prompt appears, WSL is ready to use.

`); const runInstallerCommand = `WIN_DOWNLOADS="$(wslpath "$(cmd.exe /c echo %USERPROFILE% 2>/dev/null | tr -d '\\r')")/Downloads" bash -x "$WIN_DOWNLOADS/GeneratedScript.txt" 2>&1 | tee "$WIN_DOWNLOADS/installation_log.txt"`; const runInstallerBox = (() => { const container = html`

Run the installer

Download GeneratedScript.txt.
Open WSL.
Click Copy WSL installation command below.
Paste the command into the WSL window and press Enter.

${runInstallerCommand}

The installation output will automatically be saved as installation_log.txt in your Windows Downloads folder.

If the installation stops or reports an error, upload installation_log.txt to ChatGPT or another AI assistant and ask it to analyze the error, identify the program that failed, and suggest an updated installation command or code change.

`; const button = container.querySelector("button"); const label = container.querySelector(".copy-label"); button.addEventListener("click", async () => { try { await navigator.clipboard.writeText(runInstallerCommand); label.textContent = "✅ Copied!"; setTimeout(() => { label.textContent = "📋 Copy WSL installation command"; }, 1500); } catch (error) { label.textContent = "❌ Copy failed"; setTimeout(() => { label.textContent = "📋 Copy WSL installation command"; }, 2000); } }); return container; })(); display(runInstallerBox);2f:Te25,const selectedProgramsInput = document.createElement("form"); selectedProgramsInput.innerHTML = `

Select Programs to install

${programs.map(d => ` `).join("")}

Program	Purpose	Download / installation page
${d.name}	${d.purpose}	${d.url}

`; Object.defineProperty(selectedProgramsInput, "value", { get() { return [ ...selectedProgramsInput.querySelectorAll( 'input[name="program"]:checked' ) ].map(d => d.value); } }); function notifyProgramChange() { selectedProgramsInput.dispatchEvent( new Event("input", { bubbles: true }) ); } selectedProgramsInput .querySelector(".check-all") .addEventListener("click", () => { selectedProgramsInput .querySelectorAll('input[name="program"]') .forEach(box => { box.checked = true; }); notifyProgramChange(); }); selectedProgramsInput .querySelector(".check-none") .addEventListener("click", () => { selectedProgramsInput .querySelectorAll('input[name="program"]') .forEach(box => { box.checked = false; }); notifyProgramChange(); }); selectedProgramsInput.addEventListener( "change", notifyProgramChange ); const selectedPrograms = view(selectedProgramsInput);30:T128f,const programs = [ { name: "Dorado", purpose: "Nanopore basecalling, demultiplexing, trimming, and modified-base calling", url: "https://github.com/nanoporetech/dorado", platform: "wsl", platformLabel: "Windows via WSL", env: "reads-assembly-core", special: "dorado" }, { name: "Filtlong", purpose: "Filter Nanopore reads by quality and length", url: "https://github.com/rrwick/Filtlong", platform: "wsl", platformLabel: "Windows via WSL", env: "reads-assembly-core", pkg: "filtlong" }, { name: "Flye", purpose: "Assemble Nanopore long reads into phage genomes", url: "https://github.com/mikolmogorov/Flye", platform: "wsl", platformLabel: "Windows via WSL", env: "reads-assembly-core", pkg: "flye" }, { name: "minimap2", purpose: "Map Nanopore reads back to assembled genomes", url: "https://github.com/lh3/minimap2", platform: "wsl", platformLabel: "Windows via WSL", env: "reads-assembly-core", pkg: "minimap2" }, { name: "samtools", purpose: "Sort, index, and analyze BAM alignment files", url: "https://github.com/samtools/samtools", platform: "wsl", platformLabel: "Windows via WSL", env: "reads-assembly-core", pkg: "samtools" }, { name: "Medaka", purpose: "Polish Nanopore genome assemblies", url: "https://github.com/nanoporetech/medaka", platform: "wsl", platformLabel: "Windows via WSL", env: "medaka-polish", pkg: "medaka", special: "medaka" }, { name: "Bandage", purpose: "Visualize assembly graphs produced by Flye and other assemblers", url: "https://github.com/rrwick/Bandage", platform: "wsl", platformLabel: "Windows via WSL", special: "bandage" }, { name: "NCBI BLAST+", purpose: "Compare nucleotide and protein sequences", url: "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/", platform: "wsl", platformLabel: "Windows via WSL", env: "reads-assembly-core", pkg: "blast" }, { name: "Pharokka", purpose: "Primary bacteriophage genome annotation", url: "https://github.com/gbouras13/pharokka", platform: "wsl", platformLabel: "Windows via WSL", env: "pharokka", pkg: "pharokka", post: "pharokka install" }, { name: "Phold", purpose: "Improve phage protein annotation using structural similarity", url: "https://github.com/gbouras13/phold", platform: "wsl", platformLabel: "Windows via WSL", env: "phold", pkg: "phold", post: "phold install -t 8" }, { name: "Phynteny", purpose: "Predict phage protein functions using gene synteny", url: "https://github.com/susiegriggo/Phynteny", platform: "wsl", platformLabel: "Windows via WSL", env: "phynteny", pkg: "phynteny", post: "install_models" }, { name: "Clinker", purpose: "Compare gene organization and synteny between phage genomes", url: "https://github.com/gamcil/clinker", platform: "wsl", platformLabel: "Windows via WSL", env: "clinker", pkg: "clinker-py" }, { name: "PhamClust", purpose: "Cluster related phage genomes using shared protein families", url: "https://github.com/chg60/phamclust", platform: "wsl", platformLabel: "Windows via WSL", env: "phamclust", pkg: "phamclust", special: "pip" }, { name: "MMseqs2", purpose: "Fast protein and nucleotide similarity searching and clustering", url: "https://github.com/soedinglab/MMseqs2", platform: "wsl", platformLabel: "Windows via WSL", env: "reads-assembly-core", pkg: "mmseqs2" }, { name: "HMMER", purpose: "Search proteins using profile hidden Markov models", url: "http://hmmer.org/", platform: "wsl", platformLabel: "Windows via WSL", env: "reads-assembly-core", pkg: "hmmer" }, { name: "CheckV", purpose: "Assess viral genome completeness and contamination", url: "https://github.com/chklovski/CheckV", platform: "wsl", platformLabel: "Windows via WSL", env: "checkv", pkg: "checkv" }, { name: "geNomad", purpose: "Identify and classify viral sequences", url: "https://github.com/apcamargo/genomad", platform: "wsl", platformLabel: "Windows via WSL", env: "genomad", pkg: "genomad", post: ` mkdir -p ~/databases/genomad cd ~/databases/genomad genomad download-database . cd ~ ` }, { name: "Foldseek", purpose: "Search for structurally similar proteins", url: "https://github.com/steineggerlab/foldseek", platform: "wsl", platformLabel: "Windows via WSL", env: "foldseek", pkg: "foldseek" } ];31:T6c72,const generatedScript = (() => { const lines = []; if (!needsWSL) { return "# No WSL-based programs selected."; } const hasProgram = name => selectedWSLPrograms.some(d => d.name === name); const corePackages = selectedWSLPrograms.filter( d => d.env === "reads-assembly-core" && d.pkg ); const needsCoreEnv = corePackages.length > 0 || hasProgram("Dorado"); lines.push("#!/usr/bin/env bash"); lines.push("set -Eeuo pipefail"); lines.push(""); lines.push( `trap 'status=$?; echo; echo "ERROR: installation failed at line $LINENO (exit $status)"; exit $status' ERR` ); lines.push(""); lines.push("# ==========================================="); lines.push("# Phage bioinformatics software installer"); lines.push("# Windows 11 Pro / WSL2 Ubuntu"); lines.push("# ==========================================="); lines.push(""); // ================================================== // Ubuntu utilities // ================================================== lines.push("# ==========================================="); lines.push("# Ubuntu system utilities"); lines.push("# ==========================================="); lines.push(""); lines.push( 'if sudo -n true >/dev/null 2>&1; then' ); lines.push( ' echo "Password-free sudo access detected."' ); lines.push( ' echo "Checking/installing optional Ubuntu utilities..."' ); lines.push( " sudo -n apt update" ); lines.push( " sudo -n apt install -y build-essential git wget curl tar gzip ca-certificates" ); if (hasProgram("Bandage")) { lines.push( " sudo -n apt install -y libfuse2 || true" ); } lines.push("else"); lines.push( ' echo "NOTE: sudo requires a password or is managed by your IT department."' ); lines.push( ' echo "Skipping Ubuntu system-package installation."' ); lines.push( ' echo "The Conda/Mamba bioinformatics installation will continue."' ); lines.push("fi"); lines.push(""); // ================================================== // Check essential utilities // ================================================== lines.push( "# Check that essential command-line utilities are available" ); lines.push( 'MISSING_TOOLS=""' ); lines.push( 'for cmd in curl wget tar gzip; do' ); lines.push( ' if ! command -v "$cmd" >/dev/null 2>&1; then' ); lines.push( ' MISSING_TOOLS="$MISSING_TOOLS $cmd"' ); lines.push(" fi"); lines.push("done"); lines.push(""); lines.push( 'if [ -n "$MISSING_TOOLS" ]; then' ); lines.push( ' echo "ERROR: The following required Ubuntu utilities are missing:$MISSING_TOOLS"' ); lines.push( ' echo "Because sudo access is unavailable, these must be installed by your IT department before continuing."' ); lines.push( " exit 1" ); lines.push("fi"); lines.push(""); lines.push( 'echo "Required command-line utilities are available."' ); lines.push(""); // ================================================== // Conda / Miniforge setup // ================================================== lines.push("# ==========================================="); lines.push("# Conda / Miniforge setup"); lines.push("# ==========================================="); lines.push(""); lines.push("load_conda() {"); lines.push( " if command -v conda >/dev/null 2>&1; then" ); lines.push( ' CONDA_BASE="$(conda info --base)"' ); lines.push( ' source "$CONDA_BASE/etc/profile.d/conda.sh"' ); lines.push(" return 0"); lines.push(" fi"); lines.push(""); lines.push( ' for candidate in "$HOME/miniforge3" "$HOME/miniconda3" "$HOME/miniconda" "$HOME/anaconda3"; do' ); lines.push( ' if [ -f "$candidate/etc/profile.d/conda.sh" ]; then' ); lines.push( ' source "$candidate/etc/profile.d/conda.sh"' ); lines.push(" return 0"); lines.push(" fi"); lines.push(" done"); lines.push(""); lines.push(" return 1"); lines.push("}"); lines.push(""); lines.push("if ! load_conda; then"); lines.push( ' echo "Conda was not found. Installing Miniforge..."' ); lines.push( ' wget -O "$HOME/Miniforge3.sh" "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh"' ); lines.push( ' bash "$HOME/Miniforge3.sh" -b -p "$HOME/miniforge3"' ); lines.push( ' source "$HOME/miniforge3/etc/profile.d/conda.sh"' ); lines.push( " conda init bash" ); lines.push("fi"); lines.push(""); lines.push( 'CONDA_BASE="$(conda info --base)"' ); lines.push( 'source "$CONDA_BASE/etc/profile.d/conda.sh"' ); lines.push(""); // ================================================== // Mamba // ================================================== lines.push("# Install Mamba if necessary"); lines.push( "if ! command -v mamba >/dev/null 2>&1; then" ); lines.push( " conda install -n base -c conda-forge mamba -y" ); lines.push("fi"); lines.push(""); // ================================================== // Conda environment helper // ================================================== lines.push("conda_env_exists() {"); lines.push( ` conda env list | awk '{print $1}' | grep -qx "$1"` ); lines.push("}"); lines.push(""); // ================================================== // Core environment // ================================================== if (needsCoreEnv) { lines.push("# ==========================================="); lines.push("# Core read / assembly environment"); lines.push("# ==========================================="); lines.push(""); const packages = corePackages .map(d => d.pkg) .join(" "); lines.push( 'if conda_env_exists "reads-assembly-core"; then' ); lines.push( ' echo "Updating existing reads-assembly-core environment..."' ); if (packages) { lines.push( ` mamba install -n reads-assembly-core -c conda-forge -c bioconda ${packages} -y` ); } lines.push("else"); lines.push( ' echo "Creating reads-assembly-core environment..."' ); if (packages) { lines.push( ` mamba create -n reads-assembly-core -c conda-forge -c bioconda ${packages} -y` ); } else { lines.push( " mamba create -n reads-assembly-core -c conda-forge python -y" ); } lines.push("fi"); lines.push(""); } // ================================================== // Dorado // ================================================== if (hasProgram("Dorado")) { lines.push("# ==========================================="); lines.push("# Dorado"); lines.push("# ==========================================="); lines.push(""); lines.push( "conda activate reads-assembly-core" ); lines.push(""); lines.push( 'INSTALLED_VER="none"' ); lines.push(""); lines.push( "if command -v dorado >/dev/null 2>&1; then" ); lines.push( ` RAW_VER="$(dorado --version 2>&1 | grep -Eo '[0-9]+(\\.[0-9]+)+' | head -n1 || true)"` ); lines.push( ' if [ -n "$RAW_VER" ]; then INSTALLED_VER="$RAW_VER"; fi' ); lines.push( 'elif [ -x "$CONDA_PREFIX/dorado-current/bin/dorado" ]; then' ); lines.push( ` RAW_VER="$("$CONDA_PREFIX/dorado-current/bin/dorado" --version 2>&1 | grep -Eo '[0-9]+(\\.[0-9]+)+' | head -n1 || true)"` ); lines.push( ' if [ -n "$RAW_VER" ]; then INSTALLED_VER="$RAW_VER"; fi' ); lines.push("fi"); lines.push(""); lines.push( 'echo "Installed Dorado version: $INSTALLED_VER"' ); lines.push(""); lines.push( 'LATEST_URL="$(curl -fLsS -o /dev/null -w "%{url_effective}" "https://github.com/nanoporetech/dorado/releases/latest")"' ); lines.push( 'LATEST_TAG="${LATEST_URL##*/}"' ); lines.push( 'LATEST_VER="${LATEST_TAG#v}"' ); lines.push(""); lines.push( 'echo "Latest Dorado version: $LATEST_VER"' ); lines.push(""); lines.push("version_gt() {"); lines.push( ` [ "$1" != "$2" ] && [ "$(printf '%s\\n%s\\n' "$1" "$2" | sort -V | tail -n1)" = "$1" ]` ); lines.push("}"); lines.push(""); lines.push( "NEED_DORADO=0" ); lines.push(""); lines.push( 'if [ "$INSTALLED_VER" = "none" ]; then' ); lines.push( " NEED_DORADO=1" ); lines.push( 'elif version_gt "$LATEST_VER" "$INSTALLED_VER"; then' ); lines.push( " NEED_DORADO=1" ); lines.push("fi"); lines.push(""); lines.push( 'if [ "$NEED_DORADO" -eq 1 ]; then' ); lines.push( ' echo "Installing/updating Dorado..."' ); lines.push(""); lines.push( ' WORKDIR="$CONDA_PREFIX/.dorado-install-tmp"' ); lines.push( ' rm -rf "$WORKDIR"' ); lines.push( ' mkdir -p "$WORKDIR"' ); lines.push( ' cd "$WORKDIR"' ); lines.push(""); lines.push( ' TARBALL="dorado-${LATEST_VER}-linux-x64.tar.gz"' ); lines.push( ' URL="https://cdn.oxfordnanoportal.com/software/analysis/${TARBALL}"' ); lines.push(""); lines.push( ' curl -fL --retry 3 --retry-delay 2 -o "$TARBALL" "$URL"' ); lines.push( ' tar -xzf "$TARBALL"' ); lines.push(""); lines.push( ' NEW_DIR="$CONDA_PREFIX/dorado-${LATEST_VER}-linux-x64"' ); lines.push( ' rm -rf "$NEW_DIR"' ); lines.push( ' mv "dorado-${LATEST_VER}-linux-x64" "$NEW_DIR"' ); lines.push(""); lines.push( ' ln -sfn "$NEW_DIR" "$CONDA_PREFIX/dorado-current"' ); lines.push(""); lines.push( ' mkdir -p "$CONDA_PREFIX/etc/conda/activate.d"' ); lines.push(""); lines.push( ` cat > "$CONDA_PREFIX/etc/conda/activate.d/dorado.sh" <<'EOF'` ); lines.push( 'export DORADO_HOME="$CONDA_PREFIX/dorado-current"' ); lines.push( 'export PATH="$DORADO_HOME/bin:$PATH"' ); lines.push( 'export LD_LIBRARY_PATH="$DORADO_HOME/lib:${LD_LIBRARY_PATH:-}"' ); lines.push( "EOF" ); lines.push(""); lines.push( ' export DORADO_HOME="$CONDA_PREFIX/dorado-current"' ); lines.push( ' export PATH="$DORADO_HOME/bin:$PATH"' ); lines.push( ' export LD_LIBRARY_PATH="$DORADO_HOME/lib:${LD_LIBRARY_PATH:-}"' ); lines.push(""); lines.push( ' rm -rf "$WORKDIR"' ); lines.push("else"); lines.push( ' echo "Dorado is already up to date."' ); lines.push("fi"); lines.push(""); lines.push( "dorado --version" ); lines.push( "conda deactivate" ); lines.push( 'cd "$HOME"' ); lines.push(""); } // ================================================== // Bandage // ================================================== if (hasProgram("Bandage")) { lines.push("# ==========================================="); lines.push("# Bandage"); lines.push("# ==========================================="); lines.push(""); lines.push( 'BANDAGE_DIR="$HOME/software/bandage"' ); lines.push( 'BANDAGE_EXE="$BANDAGE_DIR/Bandage_Ubuntu-x86-64_v0.9.0.AppImage"' ); lines.push( 'BANDAGE_EXTRACT_DIR="$BANDAGE_DIR/appimage-extracted"' ); lines.push( 'BANDAGE_LAUNCHER="$HOME/.local/bin/Bandage"' ); lines.push(""); lines.push( 'if [ ! -x "$BANDAGE_EXE" ]; then' ); lines.push( ' mkdir -p "$BANDAGE_DIR"' ); lines.push( ' cd "$BANDAGE_DIR"' ); lines.push(""); lines.push( ' wget -O Bandage.zip "https://github.com/rrwick/Bandage/releases/download/v0.9.0/Bandage_Ubuntu-x86-64_v0.9.0_AppImage.zip"' ); lines.push(""); lines.push( ' echo "Extracting Bandage archive with Python..."' ); lines.push( ' "$CONDA_BASE/bin/python" -m zipfile -e Bandage.zip .' ); lines.push(""); lines.push( ' chmod +x "$BANDAGE_EXE"' ); lines.push("else"); lines.push( ' echo "Bandage AppImage is already installed."' ); lines.push("fi"); lines.push(""); lines.push( 'mkdir -p "$HOME/.local/bin"' ); lines.push(""); lines.push( 'echo "Testing whether the Bandage AppImage can run directly..."' ); lines.push(""); lines.push( 'if "$BANDAGE_EXE" --help >/dev/null 2>&1; then' ); lines.push( ' echo "Bandage AppImage can run directly."' ); lines.push(""); lines.push( ' rm -f "$BANDAGE_LAUNCHER"' ); lines.push( ' ln -s "$BANDAGE_EXE" "$BANDAGE_LAUNCHER"' ); lines.push("else"); lines.push( ' echo "Bandage AppImage cannot run directly."' ); lines.push( ' echo "This commonly occurs when FUSE/libfuse2 is unavailable in WSL."' ); lines.push( ' echo "Extracting the AppImage so Bandage can run without FUSE..."' ); lines.push(""); lines.push( ' rm -rf "$BANDAGE_EXTRACT_DIR"' ); lines.push( ' mkdir -p "$BANDAGE_EXTRACT_DIR"' ); lines.push( ' cd "$BANDAGE_EXTRACT_DIR"' ); lines.push(""); lines.push( ' "$BANDAGE_EXE" --appimage-extract >/dev/null' ); lines.push(""); lines.push( ' if [ ! -x "$BANDAGE_EXTRACT_DIR/squashfs-root/AppRun" ]; then' ); lines.push( ' echo "ERROR: Bandage AppImage extraction did not produce AppRun."' ); lines.push( " exit 1" ); lines.push( " fi" ); lines.push(""); lines.push( ' rm -f "$BANDAGE_LAUNCHER"' ); lines.push(""); lines.push( ` printf '#!/usr/bin/env bash\\nexec "%s" "$@"\\n' "$BANDAGE_EXTRACT_DIR/squashfs-root/AppRun" > "$BANDAGE_LAUNCHER"` ); lines.push( ' chmod +x "$BANDAGE_LAUNCHER"' ); lines.push(""); lines.push( ' echo "Bandage launcher created using extracted AppImage."' ); lines.push("fi"); lines.push(""); lines.push( `grep -qxF 'export PATH="$HOME/.local/bin:$PATH"' "$HOME/.bashrc" || echo 'export PATH="$HOME/.local/bin:$PATH"' >> "$HOME/.bashrc"` ); lines.push(""); lines.push( 'export PATH="$HOME/.local/bin:$PATH"' ); lines.push(""); lines.push( 'cd "$HOME"' ); lines.push(""); } // ================================================== // Phynteny Transformer // ================================================== if ( hasProgram("Phynteny") || hasProgram("Phynteny Transformer") ) { lines.push("# ==========================================="); lines.push("# Phynteny Transformer"); lines.push("# ==========================================="); lines.push(""); lines.push( 'if conda_env_exists "phynteny_transformer"; then' ); lines.push( ' echo "Updating existing phynteny_transformer environment..."' ); lines.push( " mamba install -n phynteny_transformer -c conda-forge -c bioconda phynteny_transformer requests -y" ); lines.push("else"); lines.push( ' echo "Creating phynteny_transformer environment..."' ); lines.push( " mamba create -n phynteny_transformer -c conda-forge -c bioconda phynteny_transformer requests -y" ); lines.push("fi"); lines.push(""); lines.push( "conda activate phynteny_transformer" ); lines.push(""); lines.push( 'echo "Installing/updating Phynteny Transformer models..."' ); lines.push( "install_models" ); lines.push(""); lines.push( "phynteny_transformer --version || true" ); lines.push( "conda deactivate" ); lines.push(""); } // ================================================== // Other separate environments // ================================================== const separatePrograms = selectedWSLPrograms.filter( d => d.name !== "Dorado" && d.name !== "Bandage" && d.name !== "Phynteny" && d.name !== "Phynteny Transformer" && d.env !== "reads-assembly-core" ); for (const p of separatePrograms) { lines.push("# ==========================================="); lines.push(`# ${p.name}`); lines.push("# ==========================================="); lines.push(""); // ================================================== // Medaka // ================================================== if (p.special === "medaka") { lines.push( `if conda_env_exists "${p.env}"; then` ); lines.push( ` echo "Updating existing Medaka environment..."` ); lines.push( ` mamba install -n ${p.env} -c conda-forge -c bioconda medaka -y` ); lines.push("else"); lines.push( ` echo "Creating Medaka environment..."` ); lines.push( ` mamba create -n ${p.env} -c conda-forge -c bioconda medaka -y` ); lines.push("fi"); } // ================================================== // PhamClust // ================================================== else if (p.name === "PhamClust") { lines.push( 'PHAMCLUST_RECREATE=0' ); lines.push(""); lines.push( 'if conda_env_exists "phamclust"; then' ); lines.push( ' PHAMCLUST_PYTHON="$(conda run -n phamclust python -c \'import sys; print(f"{sys.version_info.major}.{sys.version_info.minor}")\' 2>/dev/null || true)"' ); lines.push(""); lines.push( ' echo "Existing PhamClust Python version: ${PHAMCLUST_PYTHON:-unknown}"' ); lines.push(""); lines.push( ' if [ "$PHAMCLUST_PYTHON" != "3.11" ]; then' ); lines.push( ' echo "PhamClust requires the Python 3.11 environment used by this installer."' ); lines.push( ' echo "Recreating the phamclust environment..."' ); lines.push( " PHAMCLUST_RECREATE=1" ); lines.push( " fi" ); lines.push("else"); lines.push( " PHAMCLUST_RECREATE=1" ); lines.push("fi"); lines.push(""); lines.push( 'if [ "$PHAMCLUST_RECREATE" -eq 1 ]; then' ); lines.push( ' if conda_env_exists "phamclust"; then' ); lines.push( " conda env remove -n phamclust -y" ); lines.push( " fi" ); lines.push(""); lines.push( " mamba create -n phamclust -c conda-forge python=3.11 pip setuptools wheel -y" ); lines.push("fi"); lines.push(""); lines.push( "conda activate phamclust" ); lines.push(""); lines.push( 'echo "Installing/updating PhamClust..."' ); lines.push( "python -m pip install --upgrade pip setuptools wheel" ); lines.push( "python -m pip install --upgrade phamclust" ); lines.push(""); lines.push( "phamclust --help >/dev/null 2>&1 || true" ); lines.push( "conda deactivate" ); } // ================================================== // Other pip-based programs // ================================================== else if (p.special === "pip") { lines.push( `if ! conda_env_exists "${p.env}"; then` ); lines.push( ` mamba create -n ${p.env} -c conda-forge python pip setuptools wheel -y` ); lines.push("fi"); lines.push(""); lines.push( `conda activate ${p.env}` ); lines.push( "python -m pip install --upgrade pip setuptools wheel" ); lines.push( `python -m pip install --upgrade ${p.pkg}` ); lines.push( "conda deactivate" ); } // ================================================== // Normal Conda installation // ================================================== else { lines.push( `if conda_env_exists "${p.env}"; then` ); lines.push( ` mamba install -n ${p.env} -c conda-forge -c bioconda ${p.pkg} -y` ); lines.push("else"); lines.push( ` mamba create -n ${p.env} -c conda-forge -c bioconda ${p.pkg} -y` ); lines.push("fi"); } lines.push(""); // ================================================== // Pharokka database // ================================================== if (p.name === "Pharokka") { lines.push( "conda activate pharokka" ); lines.push( 'PHAROKKA_DB="$HOME/databases/pharokka"' ); lines.push( 'mkdir -p "$PHAROKKA_DB"' ); lines.push( 'echo "Checking/installing Pharokka databases..."' ); lines.push( 'pharokka install -o "$PHAROKKA_DB"' ); lines.push( "conda deactivate" ); lines.push(""); } // ================================================== // Phold database // ================================================== else if (p.name === "Phold") { lines.push( "conda activate phold" ); lines.push( 'echo "Checking/installing Phold database..."' ); lines.push( "phold install -t 8" ); lines.push( "conda deactivate" ); lines.push(""); } // ================================================== // CheckV database // ================================================== else if (p.name === "CheckV") { lines.push( "conda activate checkv" ); lines.push( 'CHECKV_PARENT="$HOME/databases/checkv"' ); lines.push( 'mkdir -p "$CHECKV_PARENT"' ); lines.push(""); lines.push( `CHECKV_DB_DIR="$(find "$CHECKV_PARENT" -maxdepth 1 -type d -name 'checkv-db-*' | sort -V | tail -n1)"` ); lines.push(""); lines.push( 'if [ -z "$CHECKV_DB_DIR" ]; then' ); lines.push( ' echo "CheckV database not found. Downloading..."' ); lines.push( ' checkv download_database "$CHECKV_PARENT"' ); lines.push(""); lines.push( ` CHECKV_DB_DIR="$(find "$CHECKV_PARENT" -maxdepth 1 -type d -name 'checkv-db-*' | sort -V | tail -n1)"` ); lines.push("else"); lines.push( ' echo "Existing CheckV database found: $CHECKV_DB_DIR"' ); lines.push("fi"); lines.push(""); lines.push( 'if [ -n "$CHECKV_DB_DIR" ]; then' ); lines.push( ' export CHECKVDB="$CHECKV_DB_DIR"' ); lines.push( ` sed -i '/^export CHECKVDB=/d' "$HOME/.bashrc"` ); lines.push( ` echo "export CHECKVDB=\\"$CHECKV_DB_DIR\\"" >> "$HOME/.bashrc"` ); lines.push("else"); lines.push( ' echo "ERROR: CheckV database directory could not be located."' ); lines.push( " exit 1" ); lines.push("fi"); lines.push(""); lines.push( "conda deactivate" ); lines.push(""); } // ================================================== // geNomad database // ================================================== else if (p.name === "geNomad") { lines.push( "conda activate genomad" ); lines.push( 'GENOMAD_PARENT="$HOME/databases/genomad"' ); lines.push( 'GENOMAD_DB="$GENOMAD_PARENT/genomad_db"' ); lines.push( 'mkdir -p "$GENOMAD_PARENT"' ); lines.push(""); lines.push( 'if [ ! -d "$GENOMAD_DB" ]; then' ); lines.push( ' echo "geNomad database not found. Downloading..."' ); lines.push( ' genomad download-database "$GENOMAD_PARENT"' ); lines.push("else"); lines.push( ' echo "Existing geNomad database found: $GENOMAD_DB"' ); lines.push("fi"); lines.push(""); lines.push( "conda deactivate" ); lines.push(""); } } // ================================================== // Verification // ================================================== lines.push("# ==========================================="); lines.push("# Verify installations"); lines.push("# ==========================================="); lines.push(""); if (needsCoreEnv) { lines.push( "conda activate reads-assembly-core" ); const checks = { Dorado: "dorado --version", Filtlong: "filtlong --version", Flye: "flye --version", minimap2: "minimap2 --version", samtools: "samtools --version", "NCBI BLAST+": "blastn -version", MMseqs2: "mmseqs version", HMMER: "hmmsearch -h | head -n 2" }; for (const p of selectedWSLPrograms) { if (checks[p.name]) { lines.push(""); lines.push( `echo "Checking ${p.name}..."` ); lines.push( `${checks[p.name]} || true` ); } } lines.push(""); lines.push( "conda deactivate" ); } // ================================================== // Bandage verification // ================================================== if (hasProgram("Bandage")) { lines.push(""); lines.push( 'echo "Checking Bandage..."' ); lines.push(""); lines.push( 'if command -v Bandage >/dev/null 2>&1; then' ); lines.push( ' echo "Bandage launcher: $(command -v Bandage)"' ); lines.push( ' echo "Bandage: installed"' ); lines.push("else"); lines.push( ' echo "WARNING: Bandage launcher was not found."' ); lines.push("fi"); } // ================================================== // Phynteny Transformer verification // ================================================== if ( hasProgram("Phynteny") || hasProgram("Phynteny Transformer") ) { lines.push(""); lines.push( 'echo "Checking Phynteny Transformer..."' ); lines.push( 'conda run -n phynteny_transformer phynteny_transformer --version || true' ); } // ================================================== // PhamClust verification // ================================================== if (hasProgram("PhamClust")) { lines.push(""); lines.push( 'echo "Checking PhamClust..."' ); lines.push( 'conda run -n phamclust python --version || true' ); lines.push( 'conda run -n phamclust phamclust --help >/dev/null 2>&1 && echo "PhamClust: OK" || echo "PhamClust command could not be verified."' ); } lines.push(""); lines.push("# ==========================================="); lines.push("# Installation complete"); lines.push("# ==========================================="); lines.push(""); lines.push( 'echo "Selected phage bioinformatics software installation is complete."' ); lines.push( 'echo "Open a new WSL terminal before using newly added PATH variables."' ); return lines.join("\n"); })();32:[] 2c:{"id":"0c1498011f675e6a","slug":"untitled","title":"Phage Bioinformatics Software Installer","thumbnail":"4d460b5381178d191f1b63e8aa19a76104214d02dbe2955fd19e665535ac655c","access_level":"public","create_time":"$D2026-09-28T18:28:38.288Z","update_time":"$D2026-09-28T21:05:31.146Z","view_time":null,"first_public_time":"$D2026-09-28T18:50:04.468Z","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":135,"publish_version":135,"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":"team","id":"d1dfc5f860fb8699","login":"phage","name":"WabushOnce","avatar_url":"https://avatars-next.observableusercontent.com/9303f26b98fd8f7e04b66a6ac3218bfd2ca7e146f15ba24ca32ffac15f802763","tier":"starter_2024","role":"editor"}],"comments":[],"custom_thumbnail":false,"trashed":false,"lapsed":null,"subscribed":null,"forks":0,"collection":null,"type":"notebook","body":{"title":"Phage Bioinformatics Software Installer","cells":[{"id":1,"value":"# Phage Bioinformatics Software Installer\n","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":22,"value":"This installer is designed for a Windows 11 Pro computer using WSL (Windows Subsystem for Linux).","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":21,"value":"$2e","pinned":false,"hidden":false,"mode":"ts","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":3,"value":"$2f","pinned":false,"hidden":false,"mode":"ts","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":19,"value":"const downloadInstaller = (() => {\n const blob = new Blob(\n [generatedScript],\n { type: \"text/plain;charset=utf-8\" }\n );\n\n const url = URL.createObjectURL(blob);\n\n const link = html`\n \n ⬇️ Download GeneratedScript.txt\n \n `;\n\n return link;\n})();\n\ndisplay(downloadInstaller);","pinned":false,"hidden":false,"mode":"ts","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":15,"value":"---","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":13,"value":"const manualWindowsDisplay = html`\n

Manual Windows installation

\n\n

\n The following program is not installed by the generated WSL script.\n Install it directly in Windows.\n

\n\n

\n ${d.name} — ${d.purpose}
\n \n ${d.url}\n \n

\n`;\n\ndisplay(manualWindowsDisplay);","pinned":false,"hidden":false,"mode":"ts","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":18,"value":"---\n ## Code","pinned":false,"hidden":false,"mode":"md","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":2,"value":"$30","pinned":false,"hidden":false,"mode":"ts","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":4,"value":"const selectedObjects = programs.filter(d =>\n selectedPrograms.includes(d.name)\n);\n\nconst selectedWSLPrograms = selectedObjects.filter(\n d => d.platform === \"wsl\"\n);\n\nconst selectedWindowsPrograms = selectedObjects.filter(\n d => d.platform === \"windows\"\n);\n\nconst needsWSL = selectedWSLPrograms.length > 0;","pinned":false,"hidden":false,"mode":"ts","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":5,"value":"$31","pinned":false,"hidden":false,"mode":"ts","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"},{"id":14,"value":"const manualWindowsPrograms = [\n {\n name: \"IGV\",\n purpose: \"Graphically inspect read mappings, coverage, and genome regions\",\n url: \"https://igv.org/doc/desktop/\"\n }\n];","pinned":false,"hidden":false,"mode":"ts","author":"$undefined","summary":"$undefined","output":"$undefined","database":"$undefined"}],"files":"$W32","stdlib":"2","titling":"auto"}} 2d:"$2c:body"