merge with main pipeline gerge th otherbranch 'activeDev' of https://…

…github.com/CCBR/Pipeliner into activeDev
CCBR · Nov 20, 2018 · 5549023 · 5549023
2 parents 51b1e82 + 606964e
commit 5549023
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Showing 4 changed files with 6 additions and 1 deletion.
diff --git a/ccbrpipe.sh b/ccbrpipe.sh
@@ -3,6 +3,7 @@
 #. /usr/local/Modules/default/init/bash
 
 module load python/3.5
+module load snakemake/5.1.3
 module load graphviz
 
 export pipehome=$(dirname $0)

diff --git a/pipeline_ctrl.sh b/pipeline_ctrl.sh
@@ -1,6 +1,7 @@
 #!/bin/bash
 
 module load python/3.5
+module load snakemake/5.1.3
 
 #PBS -N PipelineTest
 

diff --git a/slurm.template b/slurm.template
@@ -2,6 +2,7 @@
 set -e
 
 module load python/3.5
+module load snakemake/5.1.3
 
 #PBS -N PipelineTest
 
@@ -34,4 +35,4 @@ mv $R/HPCusagetable.txt.tmp $R/HPC_usage_table.txt
 cd $R/Reports && $R/Reports/ngser.pl ../QC ./
 #cd $R/Reports && $R/Reports/stats2html.py
 rm -rf $R/bamstats
-rm -rf $R/*bam.cnt
+rm -rf $R/*bam.cnt
diff --git a/submit_slurm.template b/submit_slurm.template
@@ -18,6 +18,8 @@ fi
 #. /usr/local/Modules/default/init/bash
 
 module load python/3.5
+module load snakemake/5.1.3
+
 D=/home/fake
 R=/home/fake