change path to usr/local + sps option

[clitk.git] / cluster_tools / gate_run_submit_cluster.sh

diff --git a/cluster_tools/gate_run_submit_cluster.sh b/cluster_tools/gate_run_submit_cluster.sh
index 8858c68780d89832a7720f56700205bb58c93207..2ae6186bcfc38a27bfc230d4052d6c4f338e16e6 100755 (executable)
--- a/cluster_tools/gate_run_submit_cluster.sh
+++ b/cluster_tools/gate_run_submit_cluster.sh
@@ -1,4 +1,4 @@
-#!/usr/bin/env bash
+#!/bin/bash -l
 
 set -u
 SCRIPTNAME="$(basename "${0}")"
@@ -58,7 +58,7 @@ test -d ${OUTPUTDIR} || error "can't locate output dir"
 RUNID=${OUTPUTDIR##*.}
 NJOBS=${2:-"${DEFAULTNUMBEROFJOBS}"}
 NJOBSMAX=${NJOBS}
-PARAM="${4:-""}"
+PARAM="${4:-\"\"}"
 
 echo "Lets roll!!"
 echo "runid is ${RUNID}"
@@ -91,6 +91,7 @@ cp ${MACROFILE} ${OUTPUTDIR}/mac
 files=`grep "control/execute" ${MACROFILE} | cut -d " " -f 2`
 for i in $files
 do
+    echo $i
     cp $i ${OUTPUTDIR}/mac
 done
 
@@ -102,7 +103,7 @@ while test $NJOBS -gt 0; do
         PARAM=\"${PARAM}\" INDEX=${NJOBS} INDEXMAX=${NJOBSMAX} OUTPUTDIR=${OUTPUTDIR}  RELEASEDIR=${RELEASEDIR} MACROFILE=${MACROFILE} MACRODIR=${MACRODIR} PBS_JOBID="local_${NJOBS}" bash "${JOBFILE}" > ${OUTPUTDIR}/gate_${NJOBS}.log &
     elif test "$(dnsdomainname)" = "in2p3.fr"
     then
-        PROJECTGROUP=creatis 
+        PROJECTGROUP=creatis
         qsub -o "${OUTPUTDIR}" \
              -N "gate.${RUNID}" \
              -v "PARAM=\"${PARAM}\",INDEX=${NJOBS},INDEXMAX=${NJOBSMAX},OUTPUTDIR=${OUTPUTDIR},RELEASEDIR=${RELEASEDIR},MACROFILE=${MACROFILE},MACRODIR=${MACRODIR}" \