set to multi thread and send to different queues depending on seq length

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@1676 ee4ac58c-ac51-4696-9907-e4b3aa274f04

etc/run_fasta

@@ -6,7 +6,7 @@
 # to customise this script see the function called run_one_prog below
 
 
-RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_fasta,v 1.2 2004-06-11 14:54:05 tjc Exp $"
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_fasta,v 1.3 2004-06-22 10:39:58 tjc Exp $"
 
 PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
 
@@ -39,11 +39,13 @@ run_one_prog () {
     OUTPUT_FILE=$2
     DATABASE=$3
 
-
     ### change these lines:
 
+    ### get sequence size
+    seq_size=`infoseq "$INPUT_FILE" -length -only -auto | awk '{ sum += $1 } END { print sum }`
+
     FASTLIBS=/nfs/disk222/yeastpub/bio-soft/fasta/pubseqgbs export FASTLIBS
-    EXEC=/nfs/disk222/yeastpub/bio-soft/fasta/fasta33
+    EXEC=/nfs/disk222/yeastpub/bio-soft/fasta/fasta33_t
 
     echo "about to start $EXEC with input from $INPUT_FILE and output to" 1>&2
     echo "$OUTPUT_FILE using database $DATABASE" 1>&2
@@ -54,8 +56,20 @@ run_one_prog () {
     echo "command line: $COMMAND" 1>&2
 
 #    lsrun -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -v $COMMAND 2>&1 > $OUTPUT_FILE | 
-     bsub -q babelq2 -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -I $COMMAND 2>&1 > $OUTPUT_FILE |
-      tee ${PROG}_errors.new 1>&2
+
+     if [ "$seq_size" -lt 25000 ]
+     then
+       bsub -q babelq2 -n 1 -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -I $COMMAND 2>&1 > $OUTPUT_FILE |
+         tee ${PROG}_errors.new 1>&2
+     elif [ "$seq_size" -lt 70000 ]
+     then
+       bsub -q "longblastq" -n 1 -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -I $COMMAND 2>&1 > $OUTPUT_FILE |
+         tee ${PROG}_errors.new 1>&2
+     else
+       bsub -q "local_blastq" -n 1 -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -I $COMMAND 2>&1 > $O
+UTPUT_FILE |
+         tee ${PROG}_errors.new 1>&2
+     fi
 
     #### end of changes