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 \ -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
bin are linked to the root directory.
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