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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 in ~/.config/guix/channels.scm as described
-[here](https://guix.gnu.org/manual/en/html_node/Channels.html)
-
- (cons*
- (channel
- (name 'gn-bioinformatics)
- (url "https://git.genenetwork.org/pjotrp/guix-bioinformatics.git")
- (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://git.genenetwork.org/pjotrp/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
-
-# 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+