From e2ac61bfa472f23eb8e0c6863395a79c94a3d68a Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Mon, 16 Dec 2019 05:15:39 -0600
Subject: README

---
 README.org | 44 ++++++++++++++++++++++++--------------------
 1 file changed, 24 insertions(+), 20 deletions(-)

diff --git a/README.org b/README.org
index 1132850..cba626b 100644
--- a/README.org
+++ b/README.org
@@ -1,20 +1,21 @@
-# guix-bioinformatics
+* 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.
+http://genenetwork.org/.  See [[https://github.com/pjotrp/guix-notes/blob/master/HACKING.org][Guix notes]] 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)
+[[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
@@ -24,74 +25,77 @@ 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=$genenetwork/guix-bioinformatics/ ./pre-inst-env guix package -A cwl
+: env GUIX_PACKAGE_PATH=$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
+* 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
+* 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
 
-## python2-numarray 1.5.2
-
-Install python2-numarray package with
-
-    guix pull
-    guix package -i python2-numarray
-
-## Common Workflow Language (CWL)
+* 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
+* Development tips
 
-## Override individual packages
+** 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
+:    guix package --install-from-file=that-file.scm
 
 
-## LICENSE
+* LICENSE
 
 These package descriptions (so-called Guix expressions) are
 distributed by the same license as GNU Guix, i.e. GPL3+
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