diff --git a/etc/run_fasta.sanger b/etc/run_fasta.sanger
index 73fe2cdc4f7b68050b8d78f1272d0185ff14e258..5f6b5a37c4373b547013916ad3325c6bb51214be 100755
--- a/etc/run_fasta.sanger
+++ b/etc/run_fasta.sanger
@@ -6,7 +6,17 @@
 # to customise this script see the function called run_one_prog below
 
 
-RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_fasta.sanger,v 1.8 2005-11-29 10:13:07 tjc Exp $"
+RCS_HEADER="$Header: /cvsroot/pathsoft/artemis/etc/run_fasta.sanger,v 1.8 2005/11/29 10:13:07 tjc Exp $"
+
+cleanUp()
+{
+  echo $1
+  cat $1 | while thisLine=`line`
+  do
+     rm -f $thisLine
+     done 
+     rm -f $1
+}
 
 PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
 
@@ -71,11 +81,12 @@ run_one_prog () {
     ### change these lines:
 
     ### get sequence size
-    seq_size=`infoseq "$INPUT_FILE" -length -only -auto | awk '{ sum += $1 } END { print sum }`
+    seq_size=`infoseq "$INPUT_FILE" -length -only -auto | awk '{ sum += $1 } END { print sum }'`
 
-    FASTLIBS=/nfs/disk222/yeastpub/bio-soft/fasta/pubseqgbs export FASTLIBS
+    FASTLIBS=/software/pathogen/external/etc/pubseqgbs export FASTLIBS
 #   EXEC=/nfs/disk222/yeastpub/bio-soft/fasta/fasta33_t
-    EXEC=/nfs/disk222/yeastpub/bio-soft/fasta/fasta33
+#   EXEC=/nfs/disk222/yeastpub/bio-soft/fasta/fasta33
+    EXEC=/software/pathogen/external/applications/fasta/fasta35
 
     echo "about to start $EXEC with input from $INPUT_FILE and output to" 1>&2
     echo "$OUTPUT_FILE using database $DATABASE" 1>&2
@@ -118,16 +129,18 @@ local *BSUB;
 my $file     = $ARGV[0];
 my $database = $ARGV[1];
 my $pwd      = $ARGV[2];
+my $dirname  = $ARGV[3];
 chomp $file;
 chomp $database;
 
-$ENV{'FASTLIBS'} = "/nfs/disk222/yeastpub/bio-soft/fasta/pubseqgbs_test";
+$ENV{'FASTLIBS'} = "/software/pathogen/external/etc/pubseqgbs";
 
 
 open(BSUB, "| bsub -q normal -o fasta_errors -n 1 -R \"select[blast && mem > 500] rusage[r1m=1:mem=500]\" -K") or die "could not open bsub pipe : $!";
 open(LIST_FILE,$file);
 
 $EXEC="/nfs/disk222/yeastpub/bio-soft/fasta/fasta33_t";
+$EXEC="/software/pathogen/external/applications/fasta/fasta35";
 
 while(my $inFile = <LIST_FILE>)
 {
@@ -177,13 +190,16 @@ local *BSUB;
 my $file     = $ARGV[0];
 my $database = $ARGV[1];
 my $pwd      = $ARGV[2];
+my $dirname  = $ARGV[3];
+
 chomp $file;
 chomp $database;
 
-$ENV{'FASTLIBS'} = "/nfs/disk222/yeastpub/bio-soft/fasta/pubseqgbs_test";
+$ENV{'FASTLIBS'} = "/software/pathogen/external/etc/pubseqgbs";
 open(LIST_FILE,$file);
 
 $EXEC="/nfs/disk222/yeastpub/bio-soft/fasta/fasta33";
+$EXEC="/software/pathogen/external/applications/fasta/fasta35";
 $NEW_WDIR=".";
 $NUM_JOBS=0;
 
@@ -191,6 +207,8 @@ while(my $inFile = <LIST_FILE>)
 { 
   $NUM_JOBS++;
   chomp($inFile);
+ 
+  $inFile =~ s/.automount\/evs-users2\/root/nfs/;
 
   if($inFile =~ m/^($pwd)(.*)/)
   {
@@ -394,13 +412,13 @@ sub bsub
   
   push(@bsub_jobs, "$name$random\_fasta");
 
-  my $QUEUE="longblastq";
+  my $QUEUE="long";
   if($NUM_JOBS <= 6)
   {
     $QUEUE="normal";
   }
 
-  open(BSUB, "| bsub -q $QUEUE -o /dev/null -n 1 -R \"select[blast && mem > 500] rusage[mem=500]\" -J$name$random\_fasta\"[$index]%16\"")  or die "could not open bsub pipe  : $!";
+  open(BSUB, "| bsub -q $QUEUE -o /dev/null -n 1 -R \"select[mem > 500] rusage[mem=500]\" -J$name$random\_fasta\"[$index]%16\"")  or die "could not open bsub pipe  : $!";
   print BSUB "cd $NEW_WDIR\n";
   print BSUB "$EXEC -B -S -q -b 100 -H $prefix$num";
   print BSUB "\${LSB_JOBINDEX} $database ktup 2 > $prefix$num";
@@ -408,6 +426,11 @@ sub bsub
 
   print BSUB "gzip -9f $prefix$num";
   print BSUB "\${LSB_JOBINDEX}\.out\n";
+  print BSUB "zip ${dirname}fasta.zip $prefix$num";
+  print BSUB "\${LSB_JOBINDEX}\.out\.gz\n";
+  print BSUB "rm -f $prefix$num";
+  print BSUB "\${LSB_JOBINDEX}\.out\.gz\n";
+    
 
  close BSUB or die "--Could not submit job : $!";
 }
@@ -435,10 +458,13 @@ then
       CMD=`echo $PERL_PROG_1`
       ssh babel "cd $WDIR; perl -w -e '$CMD' \"$1\" \"$EXPANDED_DATABASE\" \"$PWD\""
    else
-      perl -w -e "$PERL_PROG" "$1" "$EXPANDED_DATABASE" "$PWD"
+      DIR=`dirname $PWD/$1`
+      echo $DIR
+      perl -w -e "$PERL_PROG" "$1" "$EXPANDED_DATABASE" "$PWD" "$DIR/"
    fi
 else
     run_one_prog $1 $2 $EXPANDED_DATABASE
 fi
 
+cleanUp $1
 exit 0