use flexi blast & bsub

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2803 ee4ac58c-ac51-4696-9907-e4b3aa274f04

etc/run_blastn.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_blastn.sanger,v 1.1 2005-02-21 11:42:18 tjc Exp $"
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastn.sanger,v 1.2 2005-06-09 12:48:51 tjc Exp $"
 
 PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
 
@@ -63,17 +63,16 @@ run_one_prog () {
     if [ $REMOTE = "Y" ]; then
       WDIR=`pwd`
       export WDIR
-      rsh babel "cd $WDIR; lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastn \
-                 $EXTRA_ARGS >! $OUTPUT_FILE"
+#      rsh babel "cd $WDIR; lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastn \
+#                 $EXTRA_ARGS >! $OUTPUT_FILE"
+       rsh babel "cd $WDIR;  bsub -q  longblastq -o $OUTPUT_FILE -e ${PROG}_errors.new -I flexi_blast.pl $DATABASE $INPUT_FILE $EXTRA_ARGS"
     else
-      lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastn \
-        $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
-        tee ${PROG}_errors.new 1>&2
-    fi
+#      lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastn \
+#        $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
+#        tee ${PROG}_errors.new 1>&2
 
-#   lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastn \
-#     $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 $DATABASE $INPUT_FILE $EXTRA_ARGS 
+    fi
 
     #### end of changes