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bimsbbioinfo/pigx

By bimsbbioinfo

•Updated almost 6 years ago

The complete PiGx pipeline collection.

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621

bimsbbioinfo/pigx repository overview

⁠About

This repository contains Docker images for the PiGx genomics pipeline collection. The images here were generated with GNU Guix, which is the preferred way of installing the PiGx pipelines.

PiGx is free software. For more information about PiGx see http://bioinformatics.mdc-berlin.de/pigx/⁠

⁠How it got here

The Docker image was created with this command:

guix pack pigx            \
          -f docker       \
          --save-provenance        \
          -S /bin=bin     \
          -S /lib=lib     \
          -S /share=share \
          glibc-utf8-locales tzdata coreutils bash

This means that it contains the package closure of the package pigx and coreutils, bash, locale data, and timezone data for convenience. Common directories like lib, share, and bin are linked to the root directory.

⁠Running PiGx

To run the "pigx" tool set up the container like this:

     docker run -e LC_ALL=en_US.UTF-8      \
                -e HOME=/data               \
                -e TZDIR=/share/zoneinfo    \
                -e TZ=UTC+1                 \
                -e GUIX_LOCPATH=/lib/locale \
                -e PATH=/bin                \
                -v $PWD:/data -w /data      \
                --tmpfs /tmp                \
                bimsbbioinfo/pigx:test      \
                pigx --help

Your current working directory will be available as /data.

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Last updated

almost 6 years ago

docker pull bimsbbioinfo/pigx