Merge pull request #502 from RoanKanninga/master

updated gd and gaf groups for the automation part

compute5/Automated/automated_copyDataToPrm.sh

@@ -3,8 +3,11 @@ set -u
 
 MYINSTALLATIONDIR=$( cd -P "$( dirname "$0" )" && pwd )
 
+groupname=$1
+
 ##source config file (zinc-finger.gcc.rug.nl.cfg, leucine-zipper.gcc.rug.nl OR gattaca.cfg)
 myhost=$(hostname)
+. ${MYINSTALLATIONDIR}/${groupname}.cfg
 . ${MYINSTALLATIONDIR}/${myhost}.cfg
 . ${MYINSTALLATIONDIR}/sharedConfig.cfg
 

compute5/Automated/automated_copyDataToZinc.sh

@@ -2,13 +2,14 @@ set -e
 set -u
 
 GAT=$1
-
+groupname=$2
 gattacaAddress="${GAT}.gcc.rug.nl"
 echo $gattacaAddress
 MYINSTALLATIONDIR=$( cd -P "$( dirname "$0" )" && pwd )
 
 ##source config file (zinc-finger.gcc.rug.nl.cfg, leucine-zipper.gcc.rug.nl OR gattaca.cfg)
 myhost=$(hostname)
+. ${MYINSTALLATIONDIR}/${groupname}.cfg
 . ${MYINSTALLATIONDIR}/${myhost}.cfg
 . ${MYINSTALLATIONDIR}/sharedConfig.cfg
 

compute5/Automated/sharedConfig.cfg

@@ -1,11 +1,11 @@
-WORKDIR="/groups/umcg-gaf/${tmpDirectory}"
+WORKDIR="/groups/${GROUP}/${tmpDirectory}"
 LOGDIR="${WORKDIR}/logs/"
 GENERATEDSCRIPTS=${WORKDIR}/generatedscripts
 RAWDATADIR="${WORKDIR}/rawdata/ngs/"
-RAWDATADIRPRM="/groups/umcg-gaf/prm02/rawdata/ngs/"
-SAMPLESHEETSPRMDIR="/groups/umcg-gaf/prm02/rawdata/Samplesheets"
+RAWDATADIRPRM="/groups/${GROUP}/prm02/rawdata/ngs/"
+SAMPLESHEETSPRMDIR="/groups/${GROUP}/prm02/rawdata/Samplesheets"
 SAMPLESHEETSDIR="${WORKDIR}/Samplesheets"
-GATTACA="/groups/umcg-gaf/scr01/"
+GATTACA="/groups/${GROUP}/scr01/"
 ONTVANGER="helpdesk.gcc.groningen@gmail.com"
 DNA="NGS_DNA/3.2.2-Molgenis-Compute-v16.04.1-Java-1.8.0_45"
 RNA="NGS_RNA/3.2.2-Molgenis-Compute-v15.12.4-Java-1.8.0_45"

compute5/Automated/umcg-gaf.cfg

@@ -0,0 +1 @@
+GROUP="umcg-gaf"

compute5/Automated/umcg-gd.cfg

@@ -0,0 +1 @@
+GROUP="umcg-gd"