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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.
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
git clone https://github.com/genenetwork/guix-bioinformatics.git
export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
guix package -i slurm-llnl
~/.guix-profile/sbin/slurmd -C -D
ClusterName=(null) NodeName=selinunte CPUs=4 Boards=1 SocketsPerBoard=1 CoresPerSocket=2 ThreadsPerCore=2 RealMemory=7890 TmpDisk=29909
## Module system
Install the module environment with
git clone https://github.com/genenetwork/guix-bioinformatics.git
export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
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
git clone https://github.com/genenetwork/guix-bioinformatics.git
export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
guix package -i python2-numarray
## Common Workflow Language (CWL)
Install the common workflow language tool cwltool with
git clone https://github.com/genenetwork/guix-bioinformatics.git
export GUIX_PACKAGE_PATH=$PWD/guix-bioinformatics/
guix package -i python2-cwltool
cwtool --version
1.0.20150916041152
# 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
## 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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