pscedu / singularity-vcf2maf

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

singularity-vcf2maf

Singularity recipe for vcf2maf.

Installing the container on Bridges 2

Copy the

• SIF file
• and the vcf2maf, vcf2vcf, maf2maf and maf2vcf scripts

to /opt/packages/vcf2maf/1.6.21.

Copy the file modulefile.lua to /opt/modulefiles/vcf2maf as 1.6.21.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

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