update to NGS_DNA-3.2.6

molgenis · Oct 24, 2016 · 56a25f4 · 56a25f4
1 parent bbef6a0
commit 56a25f4
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Showing 2 changed files with 5 additions and 3 deletions.
diff --git a/automated_generate_template.sh b/automated_generate_template.sh
@@ -5,7 +5,7 @@ set -u
 
 ### NEEDS 2 arguments! PROJECT AND BATCH
 
-module load NGS_DNA/3.2.5
+module load NGS_DNA/VERSIONFROMSTARTPIPELINESCRIPT
 module list 
 HOST=$(hostname)
 THISDIR=$(pwd)

diff --git a/startPipeline.sh b/startPipeline.sh
@@ -15,11 +15,11 @@ myhost=$(hostname)
 
 pipeline="dna"
 
-NGS_DNA="NGS_DNA/3.2.6"
+NGS_DNA="3.2.6"
 
 if [ "${pipeline}" == "dna" ] 
 then
-	module load ${NGS_DNA}
+	module load NGS_DNA/${NGS_DNA}
 fi
 
 count=0 
@@ -129,6 +129,8 @@ do
 			echo "copying $EBROOTNGS_AUTOMATED/automated_generate_template.sh to ${GENERATEDSCRIPTS}/${run}_${sequencer}/generate.sh" >> $LOGGER
                        	cp ${EBROOTNGS_AUTOMATED}/automated_generate_template.sh ${GENERATEDSCRIPTS}/${run}_${sequencer}/generate.sh
 
+			perl -pi -e "s|VERSIONFROMSTARTPIPELINESCRIPT|${NGS_DNA}|" ${GENERATEDSCRIPTS}/${run}_${sequencer}/generate.sh
+
 			if [ -f ${GENERATEDSCRIPTS}/${run}_${sequencer}/${run}_${sequencer}.csv ]
 			then
 				echo "${GENERATEDSCRIPTS}/${run}_${sequencer}/${run}_${sequencer}.csv already existed, will now be removed and will be replaced by a fresh copy" >> $LOGGER