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Fixing path to index file for pairend joining.

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1 parent d8f73dc commit a0014a56edf5cbc541f3b6faa3058e56a0294812 @jaredbischof jaredbischof committed Mar 25, 2013
Showing with 2 additions and 2 deletions.
  1. +2 −2 src/MGRAST/cgi/upload.cgi
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4 src/MGRAST/cgi/upload.cgi
@@ -297,13 +297,13 @@ if (scalar(@rest) && $rest[0] eq 'user_inbox') {
if($seqfile3 eq "") {
$command = "echo \"$fix_files_str $Conf::pairend_join -j -m 8 -p 10 -t $udir/.tmp -o $udir/$joinfile $udir/$seqfile1 $udir/$seqfile2 2>&1 | tee -a $udir/$seqfile1.error_log > $udir/$seqfile2.error_log; rm $lock_file1 $lock_file2 $lock_file3;\" | /usr/local/bin/qsub -q fast -j oe -N $jobid -l walltime=60:00:00 -m n -o $udir/.tmp";
} else {
- $command = "echo \"$fix_files_str $Conf::pairend_join -j -r -i $seqfile3 -m 8 -p 10 -t $udir/.tmp -o $udir/$joinfile $udir/$seqfile1 $udir/$seqfile2 2>&1 | tee -a $udir/$seqfile1.error_log > $udir/$seqfile2.error_log; rm $lock_file1 $lock_file2 $lock_file3;\" | /usr/local/bin/qsub -q fast -j oe -N $jobid -l walltime=60:00:00 -m n -o $udir/.tmp";
+ $command = "echo \"$fix_files_str $Conf::pairend_join -j -r -i $udir/$seqfile3 -m 8 -p 10 -t $udir/.tmp -o $udir/$joinfile $udir/$seqfile1 $udir/$seqfile2 2>&1 | tee -a $udir/$seqfile1.error_log > $udir/$seqfile2.error_log; rm $lock_file1 $lock_file2 $lock_file3;\" | /usr/local/bin/qsub -q fast -j oe -N $jobid -l walltime=60:00:00 -m n -o $udir/.tmp";
}
} else {
if($seqfile3 eq "") {
$command = "echo \"$fix_files_str $Conf::pairend_join -m 8 -p 10 -t $udir/.tmp -o $udir/$joinfile $udir/$seqfile1 $udir/$seqfile2 2>&1 | tee -a $udir/$seqfile1.error_log > $udir/$seqfile2.error_log; rm $lock_file1 $lock_file2 $lock_file3;\" | /usr/local/bin/qsub -q fast -j oe -N $jobid -l walltime=60:00:00 -m n -o $udir/.tmp";
} else {
- $command = "echo \"$fix_files_str $Conf::pairend_join -r -i $seqfile3 -m 8 -p 10 -t $udir/.tmp -o $udir/$joinfile $udir/$seqfile1 $udir/$seqfile2 2>&1 | tee -a $udir/$seqfile1.error_log > $udir/$seqfile2.error_log; rm $lock_file1 $lock_file2 $lock_file3;\" | /usr/local/bin/qsub -q fast -j oe -N $jobid -l walltime=60:00:00 -m n -o $udir/.tmp";
+ $command = "echo \"$fix_files_str $Conf::pairend_join -r -i $udir/$seqfile3 -m 8 -p 10 -t $udir/.tmp -o $udir/$joinfile $udir/$seqfile1 $udir/$seqfile2 2>&1 | tee -a $udir/$seqfile1.error_log > $udir/$seqfile2.error_log; rm $lock_file1 $lock_file2 $lock_file3;\" | /usr/local/bin/qsub -q fast -j oe -N $jobid -l walltime=60:00:00 -m n -o $udir/.tmp";
}
}
$jnum = `$command`;

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