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s-sajid-ali merged 1 commit into from
Mar 4, 2026
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bioinformatics #314

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18 changes: 18 additions & 0 deletions docs/hpc/06_tools_and_software/03_modules.md
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Expand Up @@ -17,3 +17,21 @@ Below is a list of modules and their associated functions:
| module avail | check what software packages are available |
| module help `<module-name>` | 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.
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