From dc3388c5af3bc5ab3e9d8097bf2813edcc042ef3 Mon Sep 17 00:00:00 2001 From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04> Date: Wed, 15 Dec 2004 12:54:46 +0000 Subject: [PATCH] deal with long pathnames git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2135 ee4ac58c-ac51-4696-9907-e4b3aa274f04 --- etc/run_fasta | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/etc/run_fasta b/etc/run_fasta index d11e66936..3ac40f705 100755 --- a/etc/run_fasta +++ b/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 1.9 2004-10-05 12:39:52 tjc Exp $" +RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_fasta,v 1.10 2004-12-15 12:54:46 tjc Exp $" PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'` @@ -146,6 +146,21 @@ while(my $inFile = <LIST_FILE>) } } +# if the filename is still long + if($inFile =~ m/^(\S{100})/) + { + if($inFile =~ m/^(\S{90,})(fasta\/\S+)/) + { + my $inFile_tmp = $1; + + if( -e $inFile_tmp ) + { + print BSUB "cd $inFile_tmp\n"; + $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"; } -- GitLab