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# 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.
To easily use the packages from this repo, simply add it to your `channels` list:
(cons*
(channel
(name 'gn-bioinformatics)
(url "https://gitlab.com/genenetwork/guix-bioinformatics")
(branch "master"))
%default-channels)
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.
git clone https://github.com/genenetwork/guix-bioinformatics.git
export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
guix package -A cwl
or using a checked out Guix repo with
env GUIX_PACKAGE_PATH=$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
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
## Module system
Install the module environment with
guix pull
guix package -i environment-modules
modulecmd --version
VERSION=3.2.10
DATE=2012-12-21
## python2-numarray 1.5.2
Install python2-numarray package with
guix pull
guix package -i python2-numarray
## Common Workflow Language (CWL)
Install the common workflow language tool cwltool with
guix pull
guix package -i python2-cwltool
cwtool --version
1.0.20150916041152
# Packages moved from here to main line GNU Guix
## LLVM D compiler
The LLVM D compiler was added to GNU Guix main stream!
guix package -i ldc
## Elixir and Erlang
Both languages have gone in to main line Guix:
guix package -i elixir
guix package -i erlang
## R/qtl
R-qtl is now part of main stream GNU Guix:
guix package -i r-qtl r
# 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+
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