Merge pull request #106 from RoanKanninga/master

added config files for automate.sh
molgenis · Feb 15, 2016 · 0b29bf4 · 0b29bf4
2 parents 7b60297 + e0a6c75
commit 0b29bf4
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Showing 3 changed files with 20 additions and 5 deletions.
diff --git a/automate_demultiplexing/automate.sh b/automate_demultiplexing/automate.sh
@@ -6,11 +6,16 @@ module load ngs-utils
 module load Python
 module list
 
-WORKDIR="/groups/umcg-gaf/scr01/"
-LOGSDIR="${WORKDIR}/logs/"
-NEXTSEQDIR="${WORKDIR}/sequencers/"
-SAMPLESHEETDIR="${WORKDIR}/Samplesheets/"
-ONTVANGER="[email protected]"
+##source config file (zinc-finger.gcc.rug.nl.cfg OR gattaca.cfg)
+myhost=$(hostname)
+if [[ $myhost == *"gattaca"* ]]
+then
+	. gattaca.cfg
+else
+	. ${myhost}
+fi
+
+
 
 ### Sequencer is writing to this location: $NEXTSEQDIR
 ### Looping through to see if all files

diff --git a/automate_demultiplexing/gattaca.cfg b/automate_demultiplexing/gattaca.cfg
@@ -0,0 +1,5 @@
+WORKDIR="/groups/umcg-gaf/scr01/"
+LOGSDIR="${WORKDIR}/logs/"
+NEXTSEQDIR="${WORKDIR}/sequencers/"
+SAMPLESHEETDIR="${WORKDIR}/Samplesheets/"
+ONTVANGER="[email protected]"
diff --git a/automate_demultiplexing/zinc-finger.gcc.rug.nl.cfg b/automate_demultiplexing/zinc-finger.gcc.rug.nl.cfg
@@ -0,0 +1,5 @@
+WORKDIR="/groups/umcg-gaf/tmp05/"
+LOGSDIR="${WORKDIR}/logs/"
+NEXTSEQDIR="${WORKDIR}/rawdata/nextseq"
+SAMPLESHEETDIR="${WORKDIR}/Samplesheets/"
+ONTVANGER="[email protected]"