use flexi_blast.pl

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2804 ee4ac58c-ac51-4696-9907-e4b3aa274f04

etc/run_blastp.sanger

@@ -6,7 +6,7 @@
 # to customise this script see the function called run_one_prog below
 
 
-RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastp.sanger,v 1.1 2005-02-21 11:45:09 tjc Exp $"
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastp.sanger,v 1.2 2005-06-09 13:06:56 tjc Exp $"
 
 PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
 
@@ -65,15 +65,17 @@ run_one_prog () {
     if [ $REMOTE = "Y" ]; then
       WDIR=`pwd`
       export WDIR
-      rsh babel "cd $WDIR; lsrun -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -v \
-                           blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastp \
-                           $EXTRA_ARGS >! $OUTPUT_FILE"
+#      rsh babel "cd $WDIR; lsrun -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -v \
+#                           blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastp \
+#                           $EXTRA_ARGS >! $OUTPUT_FILE"
+      rsh babel "bsub -q  longblastq -o $OUTPUT_FILE -e ${PROG}_errors.new -I flexi_blast.pl -p $DATABASE $INPUT_FILE $EXTRA_ARGS"
     else
     # add/change the flags to suit your site:
-      lsrun -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -v \
-        blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastp \
-        $EXTRA_ARGS 2>&1 > $OUTPUT_FILE | 
-        tee ${PROG}_errors.new 1>&2
+#      lsrun -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -v \
+#        blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastp \
+#        $EXTRA_ARGS 2>&1 > $OUTPUT_FILE | 
+#        tee ${PROG}_errors.new 1>&2
+       bsub -q  longblastq -o $OUTPUT_FILE -e ${PROG}_errors.new -I flexi_blast.pl -p $DATABASE $INPUT_FILE $EXTRA_ARGS
     fi
 
     #### end of changes