singularity-samtools

Singularity recipe for samtools.

Installing the container on Bridges 2

Copy the

• SIF file
• and the ace2sam, blast2sam.pl bowtie2sam.pl, export2sam.pl, fasta-sanitize.pl, generate_binaries.sh, interpolate_sam.pl, maq2sam-long, maq2sam-short, md5fa, md5sum-lite, novo2sam.pl, plot-ampliconstats, plot-bamstats, psl2sam.pl, sam2vcf.pl, samtools, samtools.pl, seq_cache_populate.pl, soap2sam.pl, wgsim, wgsim_eval.pl and zoom2sam.pl scripts

to /opt/packages/samtools/1.13.0

Copy the file modulefile.lua to /opt/modulefiles/samtools as 1.13.0.lua.

Building the image using the recipe

To build the image locally

Run the script build.sh to build image locally.

bash ./build.sh

To build the image remotely

Run the script rbuild.sh to build image remotely.

bash ./rbuild.sh

To run tests

To run the available tests, run the command

bash ./test.sh

Contributing

We welcome contributions to this repository. Before getting started, please review our Contributing Guide for detailed instructions and best practices.

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The Biomedical Applications Group at the Pittsburgh Supercomputing Center in the Mellon College of Science at Carnegie Mellon University.