fgcz-modules

FGCZ Module System

FGCZ uses Lmod (Lua-based environment modules) to manage software versions across Debian 12 servers.

Quick Reference

# List all available modules
module avail

# Search for specific module
module spider CellRanger

# Load a module
module load Dev/R/4.5.0

# Show loaded modules
module list

# Unload a module
module unload Dev/R

# Get module help
module help Dev/R/4.5.0

Environment Setup

# Core environment variables (set by lmod_profile)
export NGSEQ=/usr/local/ngseq
export ngsrc=$NGSEQ/srcm          # Source code directory
export ngpkg=$NGSEQ/packages      # Installed packages
export ngmdf=$NGSEQ/etc/modules   # Module files (.lua)

Module Categories

Category	Description	Examples
Dev	Development tools, languages	R/4.5.0, Python/3.12.8, jdk/21, pixi, uv
Aligner	Sequence alignment	CellRanger/10.0.0, STAR/2.7.11b, BWA/0.7.18
Assembly	Genome assemblers	SPAdes/4.0.0, hifiasm/0.25.0
QC	Quality control	FastQC/0.12.1, Trimmomatic/0.39
Tools	General bioinformatics	samtools/1.20, bcftools/1.20, Picard/3.2.0
Variants	Variant calling	GATK/4.6.1.0, SnpEff/5.2, VEP/113.4

Common Module Combinations

Single-Cell RNA-seq Analysis

module load Dev/R/4.5.0
module load Aligner/CellRanger/10.0.0

Python Data Science

module load Dev/Python/3.12.8      # Production conda env (read-only)
# OR
module load Dev/Python/3.12.8_dev  # Development env (can install packages)

Spatial Transcriptomics

module load Dev/R/4.5.0
module load Aligner/SpaceRanger/4.0.1
module load Aligner/XeniumRanger/4.0.0

Modern Package Managers

module load Dev/pixi/0.58.0   # For reproducible project environments
module load Dev/uv/0.9.12     # Fast Python package manager

See references/pixi-fgcz.md for shared cache config, PIXI_HOME, storage guidance (.pixi outside home quota), SBATCH integration, and GPU-node PATH setup.

Python Environments

Python modules use Miniforge/conda environments:

• Production (Dev/Python/X.Y.Z): Read-only, stable packages
• Development (Dev/Python/X.Y.Z_dev): Install new packages with pip

# Install packages in dev environment
module load Dev/Python/3.12.8_dev
pip install package_name

WARNING: Never modify production environments (gi_* prefix).

Installing New Modules

For installing new system modules, see references/installation-guide.md.

Server requirement: Installations must be performed on fgcz-r-029. You can SSH from any server:

ssh fgcz-r-029 'commands here'

Key steps:

1. Download/compile software to $ngpkg/Category/Name/Version/
2. Create lua module file at $ngmdf/Category/Name/Version.lua
3. Commit the lua file to git (module files are version controlled)
4. Test with module load Category/Name/Version

Git workflow (module files are in /usr/local/ngseq/etc):

ssh fgcz-r-029
cd /usr/local/ngseq/etc
git add modules/Category/Name/Version.lua
git commit -m "Add Name Version module"
git push  # Requires authentication

Troubleshooting

Module Not Found

module spider <name>  # Search all modules
module avail | grep -i <name>

Conflicting Modules

module list           # Check loaded modules
module purge          # Unload all modules
module load ...       # Load fresh

Python/Conda Issues

# Deactivate all conda envs first
for i in $(seq ${CONDA_SHLVL:-0}); do conda deactivate; done
module load Dev/Python/3.12.8

Library Path Problems

Never use LD_LIBRARY_PATH - it causes runtime issues. Use LD_RUN_PATH or LIBRARY_PATH instead.