14 Loading BRC Modules

The Bioinformatics Research Center (BRC) administers and maintains a set of common bioinformatics software packages for the BRC community to use on Hazel. We prefer to have control over the software to reduce the burden on individual users, eliminate redundant software downloads, and control software versions for reproducibility. Software is downloaded and formatted using container-mod.

14.1 Accessing the BRC Software repository

The BRC software downloads are located in /usr/local/usrapps/brc/brc_modules/

brc_modules
  ├── images/    ← .sif container images
  ├── modules/   ← TCL module files
  └── tools/     ← Program executables

These software containers can be loaded in two different ways:

Important

Do not copy this folder! Instead have your scripts/jobs point to software contained here.

14.1.1 Loading modules (recommended)

Much like how common modules can be loaded using module load <module_name>, the BRC software exists as modules in /usr/local/usrapps/brc/brc_modules/modules. The difference is that the module load command doesn’t know to search in this directory. To make these modules available, you must first run:

$ module use /usr/local/usrapps/brc/brc_modules/modules/

Now if you run module avail you should see a list of all the available BRC modules at the top.

$ module avail
------------------ /usr/local/usrapps/brc/brc_modules/modules ------------------
angsd/0.940             funannotate/1.8.17          paml/4.10.10
augustus/3.5.0          gatk4/4.6.2.0               picard/3.4.0
autodock-vina/1.1.2     gcta/1.94.1                 plink2/2.00a5.12
bbtools/39.84           gffread/0.12.9              prokka/1.15.6
bcftools/1.23.1         gtdbtk/2.7.2                raxml-ng/2.0.1
...

Now load any BRC module:

$ module load samtools/
Loading samtools/1.23.1
  Loading requirement: singularity/1.4.2-1

Warning

The module use command must be run every time you log onto hazel for the BRC modules to be available. You can edit your .bashrc profile automatically run module use upon start up. See chapter 13 bashrc for more details.

14.1.2 Using apptainer

You may also run software without loading it as a module by using the apptainer tool. First load the apptainer module:

$ module load apptainer

Now, any software image (.sif) file in the /usr/local/usrapps/brc/brc_modules/images directory can be run using the command apptainer exec which will temporarily load the software while your command is running. The basic structure is:

apptainer exex <path_to_.sif> <command>

For example, if we want to run samtools to print the help message:

$ apptainer exec /usr/local/usrapps/brc/brc_modules/images/quay.io_biocontainers_samtools:1.23.1--ha83d96e_0.sif samtools --help

Program: samtools (Tools for alignments in the SAM format)
Version: 1.23.1 (using htslib 1.23.1)

Usage:  samtools <command> [options]
...

Important

Both options for loading and using BRC software are compatible with bash scripts and job submission. Never do computationally expensive work from the login nodes.

14.2 Requesting software

Perhaps you want to use a software package that is missing from the BRC library, or need a package updated to a newer version. Contact the BRC at ncstate_brc@ncsu.edu with:

Software package name
Link to software package
Specific software version (if applicable)

Note

COMING SOON: Web form for software package requests.