base version sge

submit_to_cluster.sh

@@ -0,0 +1,42 @@
+#!/bin/bash
+#$ -cwd
+#$ -l h_vmem=1G
+# -l nice_cpu=1
+# -m ea
+
+
+# -l h_cpu=2:0:0 
+# -l h_rt=3:0:0 
+
+
+
+export PATH=/home/miladim/miniconda2/bin:$PATH
+export PYTHONNOUSERSITE=True
+source activate mutarna
+
+# all parameters for the shell script
+script=$1
+shift
+
+## after shifting perscript is invoked for each parameter set
+
+
+if [ -z "$SGE_TASK_ID" ]; then
+	echo "No SGE environment found! Set SGE_TASK_ID to 0!"
+	let SGE_TASK_ID=0
+fi
+
+if [ -z "$JOB_ID" ]; then
+        echo "No SGE environment found! Set JOB_ID to 1!"
+	        let JOB_ID=1
+fi
+
+if ! [ -z "$PBS_JOBID" ]; then
+        echo "PBS environment found instead of SGE! Set JOB_ID to PBS_JOBID!"
+	        let JOB_ID=$PBS_JOBID
+fi
+
+
+params=$@;
+$script $params $(expr $SGE_TASK_ID - 1)
+