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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+