* guix-bioinformatics

Bioinformatics packages for GNU Guix that are used in
http://genenetwork.org/ and some other places.  See [[https://gitlab.com/pjotrp/guix-notes/blob/master/HACKING.org][Guix notes]] for
installing and hacking GNU Guix. Other channels of bioinformatics
interest can be found at

1. https://github.com/BIMSBbioinfo
2. https://github.com/UMCUGenetics/guix-additions
3. https://github.com/ekg/guix-genomics

To easily use the packages from this repo, simply add it to your
`channels` list in ~/.config/guix/channels.scm as described
[[https://guix.gnu.org/manual/en/html_node/Channels.html][here]]:

#+BEGIN_SRC scheme
    (cons*
      (channel
        (name 'gn-bioinformatics)
        (url "https://git.genenetwork.org/pjotrp/guix-bioinformatics.git")
        (branch "master"))
      %default-channels)
#+END_SRC

and run `guix pull` like normal to update your software. This is the
recommended way to use the software from this repository and the code
snippets in this README assume you have done so.

If you want to make changes to the packages in this repo then simply set
the GUIX_PACKAGE_PATH to point to the root of this directory
before running Guix. E.g.

#+BEGIN_SRC bash
    git clone https://git.genenetwork.org/pjotrp/guix-bioinformatics.git
    export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
    guix package -A cwl
#+END_SRC

or using a checked out Guix repo with

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

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

* Slurm and munge

Install slurm with

#+BEGIN_SRC bash
    guix pull
    guix package -i slurm-llnl

    ~/.guix-profile/sbin/slurmd -C -D
      ClusterName=(null) NodeName=selinunte CPUs=4 Boards=1 SocketsPerBoard=1 CoresPerSocket=2 ThreadsPerCore=2 RealMemory=7890 TmpDisk=29909
#+END_SRC

* Module system

Install the module environment with

#+BEGIN_SRC bash
    guix pull
    guix package -i environment-modules

    modulecmd --version
      VERSION=3.2.10
      DATE=2012-12-21
#+END_SRC

* Common Workflow Language (CWL)

Install the common workflow language tool cwltool with

#+BEGIN_SRC bash
    guix pull
    guix package -i python2-cwltool

    cwtool --version
      1.0.20150916041152
#+END_SRC

* Development tips

** Override individual packages

The cheerful way of overriding a version of a package:

#+BEGIN_SRC scheme
    (use-modules (guix) (gnu packages emacs))

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

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+