submit multiple jobs at same time

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@1711 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 1.5 2004-07-08 15:28:02 tjc Exp $"
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_fasta,v 1.6 2004-07-12 12:59:22 tjc Exp $"
 
 PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
 
@@ -90,17 +90,52 @@ run_one_prog () {
     fi
 }
 
+PERL_PROG='
+
+local *BSUB;
+
+my $file     = $ARGV[0];
+my $database = $ARGV[1];
+my $pwd      = $ARGV[2];
+chomp $file;
+chomp $database;
+
+$ENV{'FASTLIBS'} = "/nfs/disk222/yeastpub/bio-soft/fasta/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";
+
+while(my $inFile = <LIST_FILE>)
+{
+  chomp($inFile);
+
+  if($inFile =~ m/^($pwd)(.*)/)
+  {
+    $inFile = $2;
+    if($inFile =~ m/^(\/)(.*)/)
+    {
+      $inFile = $2;
+    }
+  }
+  
+  print BSUB "$EXEC -B -S -q -b 100 -H $inFile $database ktup 2 > $inFile\.out\n";
+  print BSUB "gzip -9 $inFile\.out\n";
+}
+close BSUB or die "Could not submit job : $!";
+close LIST_FILE;
+
+'
+
 (echo "#!/bin/sh -"; echo "kill $$") > $PROG.kill
 
 chmod a+x $PROG.kill
 
 if [ x$ONEFILE = x ]
 then
-    for i in `cat $1`
-    do
-        run_one_prog $i $i.out $EXPANDED_DATABASE
-    done
-
+    perl -w -e "$PERL_PROG" "$1" "$EXPANDED_DATABASE" "$PWD"
 else
     run_one_prog $1 $2 $EXPANDED_DATABASE
 fi