# guix-bioinformatics

Bioinformatics packages for GNU Guix that are used in http://genenetwork.org/.
See [Guix Notes](https://github.com/pjotrp/guix-notes/blob/master/HACKING.org) for hacking GNU Guix.

Set the GUIX_PACKAGE_PATH to point to the root of this directory
before running Guix. E.g.

    env GUIX_PACKAGE_PATH=$genenetwork/guix-bioinformatics/ guix package -A cwl

or from the checked out Guix repo

    env GUIX_PACKAGE_PATH=$genenetwork/guix-bioinformatics/ ./pre-inst-env guix package -A cwl

Some of these package definitions should make it upstream into the GNU
Guix repository when tested and stable.

## Specific packages

Install the common workflow language tool cwltool with

    env GUIX_PACKAGE_PATH=$genenetwork/guix-bioinformatics/ ./pre-inst-env guix package -i python2-cwltool