From 8a66ab55cab786acb9cba38b387bbbc58fa35dfa Mon Sep 17 00:00:00 2001
From: pjotrp
Date: Sat, 21 Nov 2020 10:43:24 +0000
Subject: Updated CWL

---
 README.org | 60 +++++++++++++++++++++++++++++++++++++++++++++++++-----------
 1 file changed, 49 insertions(+), 11 deletions(-)

(limited to 'README.org')

diff --git a/README.org b/README.org
index 6f986c0..e3770f7 100644
--- a/README.org
+++ b/README.org
@@ -58,31 +58,69 @@ Install slurm with
       ClusterName=(null) NodeName=selinunte CPUs=4 Boards=1 SocketsPerBoard=1 CoresPerSocket=2 ThreadsPerCore=2 RealMemory=7890 TmpDisk=29909
 #+END_SRC
 
-* Module system
 
-Install the module environment with
+* Common Workflow Language (CWL)
+
+Install the common workflow language tool cwltool from this repo with
 
 #+BEGIN_SRC bash
+
     guix pull
-    guix package -i environment-modules
+    export PATH=$HOME/.config/guix/current/bin/guix:$PATH
+    ~/guix-bioinformatics$ env GUIX_PACKAGE_PATH=.:../guix-past/modules/ ~/.config/guix/current/bin/guix package -i cwl-runner -p ~/opt/CWL
 
-    modulecmd --version
-      VERSION=3.2.10
-      DATE=2012-12-21
+The following package will be installed:
+   cwl-runner 1.0
+
+The following derivations will be built:
+   /gnu/store/ld59374zr45rbqanh7ccfi2wa4d5x4yl-cwl-runner-1.0.drv
+   /gnu/store/86j15mxj5zp3k3sjimhqhb6zsj19azsf-python-schema-salad-7.0.20200811075006.drv
+   /gnu/store/0q2ls0is3253r4gx6hs7kmvlcz412lh1-schema-salad-7.0.20200811075006.tar.gz.drv
+   /gnu/store/myj1365ph687ynahjhg6zqslrmd6zpjq-cwltool-3.0.20201117141248.drv
+
+source ~/opt/CWL/etc/profile
+cwltool --version
+  /gnu/store/50mncjcgc8vmq5dfrh0pb82avbzy8c4r-cwltool-3.0.20201117141248/bin/.cwltool-real 3.0
 #+END_SRC
 
-* Common Workflow Language (CWL)
+To run CWL definitions you can install tools in a Guix environment (avoiding
+Docker). Say you need mafft in a workflow
+
+#+begin_src sh
+    ~/guix-bioinformatics$ env GUIX_PACKAGE_PATH=.:../guix-past/modules/ ~/.config/guix/current/bin/guix environment \
+       guix --ad-hoc cwl-runner mafft
+#+end_src
 
-Install the common workflow language tool cwltool with
+in the new shell you should be able to find both CWL and MAFFT:
+
+#+begin_src sh
+ls $GUIX_ENVIRONMENT/bin/cwl*
+/gnu/store/bhfc5rk29s38w9kgcl4zmcdlh369y9f9-profile/bin/cwl-runner
+/gnu/store/bhfc5rk29s38w9kgcl4zmcdlh369y9f9-profile/bin/cwltool
+ls $GUIX_ENVIRONMENT/bin/mafft
+/gnu/store/bhfc5rk29s38w9kgcl4zmcdlh369y9f9-profile/bin/mafft
+#+end_src
+
+The paths can be loaded into the shell with
+
+: source $GUIX_ENVIRONMENT/etc/profile
+
+* Module system
+
+For those who think they need modules: install the module environment
+with
 
 #+BEGIN_SRC bash
     guix pull
-    guix package -i python2-cwltool
+    guix package -i environment-modules
 
-    cwtool --version
-      1.0.20150916041152
+    modulecmd --version
+      VERSION=3.2.10
+      DATE=2012-12-21
 #+END_SRC
 
+Note that GNU Guix supercedes module functionality!
+
 * Development tips
 
 ** Override individual packages
-- 
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