From 7ee73ad2ecf80f28916daf9fc1bd451a13dd5d3a Mon Sep 17 00:00:00 2001
From: Curtis Hendrickson <curtish@uab.edu>
Date: Tue, 12 May 2020 14:27:48 -0500
Subject: [PATCH] Issue #5, #6: carry over fixes to most recent version of
 snakemake

Also start loading dvctools first, to avoid GCC conflicts caused when it's loaded 2nd.
---
 modulefiles/snakemakeslurm/5.9.1-4 | 46 ++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 modulefiles/snakemakeslurm/5.9.1-4

diff --git a/modulefiles/snakemakeslurm/5.9.1-4 b/modulefiles/snakemakeslurm/5.9.1-4
new file mode 100644
index 0000000..8921584
--- /dev/null
+++ b/modulefiles/snakemakeslurm/5.9.1-4
@@ -0,0 +1,46 @@
+#%Module1.0##################################################################### 
+##
+## snakemakeslurm
+##
+## https://github.com/rusalkaguy/snakemake-slurm-module
+##
+################################################################################
+set components [ file split [ module-info name ] ]
+set prog [ lindex $components 0 ]
+set snakemake-version [ lindex [ split [ lindex $components 1 ] - ] 0 ]
+set script_version [ lindex [ split [ lindex $components 1 ] - ] 1 ]
+set version ${snakemake-version}-${script_version}
+set modroot /share/apps/ngs-ccts/${prog}/${prog}-${version}
+set url	https://github.com/rusalkaguy/snakemake-slurm-module
+
+proc ModulesHelp { } {
+    global version modroot
+    puts stderr "\tsnakemakeslurm - have snakemake submit jobs via slurm to cheaha"
+   puts stderr "\n\tComponents $components\n"
+    puts stderr "\n\tVersion $version\n"
+    puts stderr "\n\tmodroot $modroot\n"
+}
+module-whatis   "Loads snakemakeslurm environment with Anaconda and Singularity support."
+
+
+#
+# load required modules
+#
+
+# make sure to load dvctools first; if loaded second, it loads an older GCC.
+module load dvctools
+# UAB-HPC old module naming convention
+# #module load rc/snakemake/${snakemake-version}
+# load Singularity (GCC-based) first - else it will mess up Snakemake's python path
+module load Singularity/3.5.2-GCC-5.4.0-2.26
+module load Anaconda3/2020.02
+module load snakemake/${snakemake-version}-foss-2018b-Python-3.6.6
+# only one version at a time
+#conflict multiqc
+
+#
+#
+# Make the directories available
+prepend-path PATH        $modroot/
+#prepend-path MANPATH 	$modroot/share/man
+#prepend-path    PYTHONPATH  odroot/lib/python2.7/site-packages