From bbef6a0a6a065aa51a2c5bf06fe243d0a18a014f Mon Sep 17 00:00:00 2001
From: RoanKanninga <roankanninga@gmail.com>
Date: Mon, 24 Oct 2016 09:12:58 +0200
Subject: [PATCH 1/2] update to 3.2.6

---
 startPipeline.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/startPipeline.sh b/startPipeline.sh
index 14b3dc8f..157f9ece 100755
--- a/startPipeline.sh
+++ b/startPipeline.sh
@@ -15,7 +15,7 @@ myhost=$(hostname)
 
 pipeline="dna"
 
-NGS_DNA="NGS_DNA/3.2.5"
+NGS_DNA="NGS_DNA/3.2.6"
 
 if [ "${pipeline}" == "dna" ] 
 then

From 56a25f4a42a2a68f6f1da6b2cc5a093b5aa85156 Mon Sep 17 00:00:00 2001
From: RoanKanninga <roankanninga@gmail.com>
Date: Mon, 24 Oct 2016 09:25:49 +0200
Subject: [PATCH 2/2] update to NGS_DNA-3.2.6

---
 automated_generate_template.sh | 2 +-
 startPipeline.sh               | 6 ++++--
 2 files changed, 5 insertions(+), 3 deletions(-)

diff --git a/automated_generate_template.sh b/automated_generate_template.sh
index 1f14e83b..9d15945f 100755
--- 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
index 157f9ece..cd79db37 100755
--- 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