Lmod¶

We use Lmod (Lua-based Environment Modules) on our cluster to manage software environments. Lmod allows users to easily load, unload, and switch between different software packages and versions.

Note

A large number of modules are installed on the cluster and are available on demand, making it easy to access the tools you need for your work.

Installed Modules¶

You can view all available software modules on the cluster using the following command.

module avail  # Flat list for the hierarchy level.

Finding Module¶

module keyword chemistry mpi   # By keyword across name, description, tags.
module spider Python/3.10      # By exact version and dependencies.

Loading Module¶

module load SAMtools/1.21

Now you will be able to use tools included in the module.

samtools --version

samtools 1.21
Using htslib 1.21

Unloading Module¶

You can unload specific module by command below.

module unload SAMtools

Resetting Modules¶

You can reset all modules loaded in environment by command below.

module reset

Example¶

Following PBS batch script submits a job called samtools_demo that requests one node with eight CPU cores, 16 GB of memory, and a two-hour wall-time limit. It resets the environment, loads the SAMtools/1.21 module, and defines input/output BAM filenames. The job then sorts the BAM file using eight threads, creates an index for random access, and generates a quick mapping-quality report with flagstat.

#!/bin/bash
#PBS -N samtools_demo                 # Job name
#PBS -l select=1:ncpus=8:mem=16gb     # One node, 8 cores, 16 GB RAM
#PBS -l walltime=02:00:00             # Max run time (hh:mm:ss)

module reset                          # Reset evironment
module load SAMtools/1.21             # Load the actual tool

INPUT_BAM=my_sample.bam
SORTED_BAM=my_sample.sorted.bam

# Coordinate-sort (8 threads, 2 GB/thread)
samtools sort -@ 8 -m 2G -o "$SORTED_BAM" "$INPUT_BAM"

# Index for random access
samtools index "$SORTED_BAM"

# Quick QC summary
samtools flagstat "$SORTED_BAM" > my_sample.flagstat.txt