Commit c304f148 authored by Malte Herold's avatar Malte Herold
Browse files

passive job did not work

parent 215069fc
......@@ -3,7 +3,7 @@
CMD_LAUNCH="oarsub -l walltime=5"
ROOTOUT="/mnt/nfs/projects/ecosystem_biology/COSMIC/IMP_output/Cosmic_new/Linking_cdhit975"
ROOTOUT="/mnt/nfs/projects/ecosystem_biology/COSMIC/IMP_output/Cosmic_new/Linking_cdhit975_additionalMG"
cat ${ROOTOUT}/samples.txt | grep -v "^#" | while read DATA
......@@ -13,13 +13,12 @@ do
OUTDIR="${ROOTOUT}/${PATIENT}"
SAMPLELIST=`dir $INDIR | tr "\t" "\n" | tr " " "\n" | grep -P "^[MV]" | tr "\n" " " `
CMD="./execution_linking.sh \"$SAMPLELIST\" $INDIR $OUTDIR"
echo $CMD
echo "$CMD_LAUNCH -n \"${PATIENT}_linking\" \"$CMD\""
$CMD_LAUNCH -n "${PATIENT}_linking" "$CMD"
# $CMD_LAUNCH -n "${PATIENT}_linking" "$CMD"
done
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