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nextflow_setup.sh

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+#!/usr/bin/env bash
+#
+# HPC & Nextflow setup script
+#
+# This script installs Nextflow and SquashFS, updates the bash configuration
+# to load required modules and sets up environment variables for HPC usage.
+#
+
+# ------------------------------------------------------------------------------
+# Configurable Variables (adjust as needed)
+# ------------------------------------------------------------------------------
+SQUASHFS_VERSION="4.6.1"
+SQUASHFS_TARBALL="squashfs${SQUASHFS_VERSION}.tar.gz"
+SQUASHFS_URL="https://sourceforge.net/projects/squashfs/files/squashfs/squashfs${SQUASHFS_VERSION}/squashfs${SQUASHFS_VERSION}.tar.gz/download"
+NXF_PIPELINE="nf-core/rnaseq"
+
+# ------------------------------------------------------------------------------
+# Strict Error Handling
+# ------------------------------------------------------------------------------
+set -euo pipefail
+
+# ------------------------------------------------------------------------------
+# Helper Functions
+# ------------------------------------------------------------------------------
+log() {
+    echo "[$(date +'%Y-%m-%d %H:%M:%S')] $*" >&2
+}
+
+# Safely source environment modules if available
+load_modules() {
+    if type module &> /dev/null; then
+        # Adjust to your system's modules initialization script if needed
+        if [ -f /etc/profile.d/modules.sh ]; then
+            source /etc/profile.d/modules.sh
+        fi
+        module load python/3.9.6 || true
+        module load singularity/3.8.5 || true
+        module load java/jdk-17.0.12 || true
+        module load java/jdk-11.0.14 || true
+    else
+        log "WARNING: Environment modules not found or not loaded!"
+        log "Skipping module loads. Please ensure Java, Python, Singularity are available."
+    fi
+}
+
+# ------------------------------------------------------------------------------
+# Functions
+# ------------------------------------------------------------------------------
+install_nextflow() {
+    log "Installing Nextflow..."
+
+    # Make sure we have Java available (from modules or system)
+    if ! command -v java &>/dev/null; then
+        log "Java not found! Aborting Nextflow installation."
+        exit 1
+    fi
+
+    # Create necessary directories
+    mkdir -p "$HOME/.local/bin" "${SCRATCH:-/tmp}/cache"
+
+    # Download Nextflow
+    curl -fsSL https://get.nextflow.io | bash
+    chmod +x nextflow
+    mv nextflow "$HOME/.local/bin/"
+
+    # Verify Nextflow installation
+    if ! "$HOME/.local/bin/nextflow" -version; then
+        log "Error: Nextflow installation failed"
+        exit 1
+    fi
+}
+
+update_environment() {
+    log "Updating environment configuration..."
+
+    # Backup existing .bashrc if it exists
+    if [ -f "$HOME/.bashrc" ]; then
+        cp "$HOME/.bashrc" "$HOME/.bashrc.backup_$(date +'%Y%m%d_%H%M%S')"
+    fi
+
+    # Only append if not already present
+    if ! grep -q "### HPC Nextflow Environment ###" "$HOME/.bashrc" 2>/dev/null; then
+        cat >> "$HOME/.bashrc" <<'EOL'
+
+### HPC Nextflow Environment ###
+export PATH="$HOME/.local/bin:$PATH"
+export NXF_SINGULARITY_CACHEDIR="${SCRATCH:-/tmp}/cache"
+
+# (Optional) Additional HPC modules or paths can be placed here:
+# module load python/3.9.6
+# module load singularity/3.8.5
+# module load java/jdk-17.0.12
+# module load java/jdk-11.0.14
+
+# Check if .local/bin is in PATH, else add it
+if [[ ":$PATH:" != *":$HOME/.local/bin:"* ]]; then
+    export PATH="$HOME/.local/bin:$PATH"
+fi
+
+EOL
+        log "Appended Nextflow HPC environment config to .bashrc."
+    else
+        log "Nextflow HPC environment config already in .bashrc. Skipping append."
+    fi
+
+    # Source updated configuration
+    # (NOTE: This will affect the current shell. If you run in a non-interactive
+    #  environment, you may need to open a new shell or manually source it again.)
+    source "$HOME/.bashrc"
+}
+
+install_squashfs() {
+    log "Installing SquashFS version $SQUASHFS_VERSION..."
+
+    # Create temporary download directory
+    TEMP_DIR=$(mktemp -d)
+    pushd "$TEMP_DIR" >/dev/null
+
+    # Download and compile SquashFS
+    wget -O "$SQUASHFS_TARBALL" "$SQUASHFS_URL"
+    tar -xzf "$SQUASHFS_TARBALL"
+    cd "squashfs-tools-$SQUASHFS_VERSION/squashfs-tools"
+
+    make
+
+    # Install binaries
+    mkdir -p "$HOME/.local/bin"
+    cp mksquashfs unsquashfs "$HOME/.local/bin/"
+
+    # Verify installation
+    if ! "$HOME/.local/bin/mksquashfs" -version; then
+        log "Error: SquashFS installation failed"
+        exit 1
+    fi
+
+    # Cleanup
+    popd >/dev/null
+    rm -rf "$TEMP_DIR"
+
+    log "SquashFS installed successfully in $HOME/.local/bin."
+}
+
+pull_nextflow_pipeline() {
+    local pipeline_path="$HOME/.nextflow/assets/$NXF_PIPELINE"
+
+    log "Checking Nextflow pipeline: $NXF_PIPELINE..."
+    if [ ! -d "$pipeline_path" ]; then
+        log "Pipeline not found. Pulling $NXF_PIPELINE..."
+        # Ensure updated environment is loaded
+        source "$HOME/.bashrc"
+
+        if ! nextflow pull "$NXF_PIPELINE"; then
+            log "Error: Failed to pull pipeline $NXF_PIPELINE"
+            exit 1
+        fi
+    else
+        log "Pipeline $NXF_PIPELINE already exists at $pipeline_path."
+    fi
+}
+
+# ------------------------------------------------------------------------------
+# Main
+# ------------------------------------------------------------------------------
+main() {
+    log "Starting HPC & Nextflow environment setup..."
+
+    # Load modules if environment modules are available
+    load_modules
+
+    install_nextflow
+    update_environment
+    install_squashfs
+    pull_nextflow_pipeline
+
+    log "HPC and Nextflow environment setup completed successfully!"
+}
+
+main