# 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 installing and hacking GNU Guix.

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

    git clone https://github.com/genenetwork/guix-bioinformatics.git
    export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
    guix package -A cwl

or using a 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.

## Install Common Workflow Language (CWL)

Install the common workflow language tool cwltool with

    git clone https://github.com/genenetwork/guix-bioinformatics.git
    export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
    guix package -i python2-cwltool
    cwtool --version
      1.0.20150916041152

## Install R/qtl

R-qtl is part of main stream GNU Guix:

    guix package -i r-qtl r
    R
      library(qtl)

# Development tips

## Override individual packages

The cheerful way of overriding a version of a package:

    (use-modules (guix) (gnu packages emacs))

    (package
      (inherit emacs)
      (name "emacs-snapshot")
      (source "/path/to/some-file-or-directory.tar.gz"))

and then run:

    guix package --install-from-file=that-file.scm


## LICENSE

These package descriptions (so-called Guix expressions) are
distributed by the same license as GNU Guix, i.e. GPL3+