Public Repository

Last pushed: 4 months ago
Short Description
The complete PiGx pipeline collection.
Full Description


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

How it got here

The Docker image was created with this command:

guix pack pigx            \
          -f docker       \
          -C none         \
          -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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