From ade369a7ab2d5448448f536bfa0305f0f15bd3f7 Mon Sep 17 00:00:00 2001 From: Sajid Ali Date: Wed, 4 Mar 2026 13:23:12 -0500 Subject: [PATCH] bioinformatics modified: docs/hpc/06_tools_and_software/03_modules.md --- docs/hpc/06_tools_and_software/03_modules.md | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/docs/hpc/06_tools_and_software/03_modules.md b/docs/hpc/06_tools_and_software/03_modules.md index 9cc5fa43f4..e3e3c4ee35 100644 --- a/docs/hpc/06_tools_and_software/03_modules.md +++ b/docs/hpc/06_tools_and_software/03_modules.md @@ -17,3 +17,21 @@ Below is a list of modules and their associated functions: | module avail | check what software packages are available | | module help `` | A module file may include more detailed help for the software package | + +## Bioinformatics modules +Common bioinformatics packages are made available via wrapper scripts that can be loaded as modules. Users can then invoke individual programs through that wrapper. +```bash +/share/apps/bioinformatics/20260224/run-bioinformatics.bash which samtools +/ext3/mamba/envs/bioinformatics/bin/samtools + +/share/apps/bioinformatics/20260224/run-bioinformatics.bash which vcftools +/ext3/mamba/envs/bioinformatics/bin/vcftools +``` + +Alternatively, load the module to get these tools on your `$PATH`. This approach keeps the user experience consistent while allowing us to manage the underlying environments through containers. + +You can list the packages available within each bioinformatics stack by running: +```bash +/share/apps/bioinformatics/20260224/bin/run-bioinformatics micromamba list +``` +It will print a list of packages within that `micromamba` environment.