From 5d4d2f07b5ac6e842a49ba977e95ff3b68aa0bb0 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 25 May 2010 11:38:14 +0000
Subject: [PATCH] fixes
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@13902 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
etc/run_fasta.sanger | 22 ++++++++--------------
1 file changed, 8 insertions(+), 14 deletions(-)
diff --git a/etc/run_fasta.sanger b/etc/run_fasta.sanger
index 89d7dc78c..c8ff05454 100755
--- a/etc/run_fasta.sanger
+++ b/etc/run_fasta.sanger
@@ -8,16 +8,6 @@
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/'`
@@ -295,6 +285,13 @@ if(defined @jobs100000)
for($count = 0; $count < @bsub_jobs; $count++)
{
open(BSUB, "| bsub -q normal -R \"select[mem > 1] rusage[mem=1]\" -o /dev/null -e /dev/null -w \"ended($bsub_jobs[$count])\" -K -J \"$bsub_jobs[$count]\_fin\"") or die "could not open bsub pipe : $!";
+
+ if($count == @bsub_jobs-1)
+ {
+ print BSUB "find ${dirname} -maxdepth 1 -name \"\*out.gz\" -print | xargs zip -j ${dirname}fasta.zip\n";
+ print BSUB "find ${dirname} -maxdepth 1 -name \"\*out.gz\" -print | xargs rm -f\n";
+ }
+
print BSUB "\"echo finished > /dev/null\" > /dev/null 2> /dev/null";
close BSUB; # or die "--Could not submit job : $!";
}
@@ -426,10 +423,8 @@ sub bsub
print BSUB "gzip -9f $prefix$num";
print BSUB "\${LSB_JOBINDEX}\.out\n";
- print BSUB "zip -j ${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";
+ print BSUB "\${LSB_JOBINDEX}\n";
close BSUB or die "--Could not submit job : $!";
@@ -466,5 +461,4 @@ else
run_one_prog $1 $2 $EXPANDED_DATABASE
fi
-cleanUp $1
exit 0
--
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