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Commit 752547e7 authored by tjc's avatar tjc
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allow to run from deskpro

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@1917 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent f5a7f2cd
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...@@ -4,7 +4,7 @@ ...@@ -4,7 +4,7 @@
# contents of files listed in a file of filenames # contents of files listed in a file of filenames
RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_clustalx,v 1.1 2004-06-09 10:03:01 tjc Exp $" RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_clustalx,v 1.2 2004-10-05 15:21:47 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'` PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
...@@ -21,7 +21,7 @@ chmod a+x $PROG.kill ...@@ -21,7 +21,7 @@ chmod a+x $PROG.kill
file_of_filenames=$1 file_of_filenames=$1
date=`date +"%y_%m_%d"` date=`date +"%y_%m_%d"`
hostname=`hostname` hostname=`hostname`
temp_file_name=/tmp/artemis_temp.$$.$hostname.$date.clustalx_input.fasta temp_file_name=clustalx/artemis_temp.$$.$hostname.$date.clustalx_input.fasta
cat $file_of_filenames | xargs cat > $temp_file_name cat $file_of_filenames | xargs cat > $temp_file_name
...@@ -36,6 +36,24 @@ perl -pne 'if (/^>(\S+)/) { ...@@ -36,6 +36,24 @@ perl -pne 'if (/^>(\S+)/) {
} }
}' $temp_file_name > $temp_file_name.processed }' $temp_file_name > $temp_file_name.processed
# delete it at some point
echo "rm -f $temp_file_name* > /dev/null 2>&1" | at now + 8 hours
HOSTNAME=`hostname`
REMOTE=N
case $HOSTNAME in
deskpro*)
REMOTE=Y ;;
*)
esac
if [ $REMOTE = "Y" ]; then
WDIR=`pwd`
export WDIR
ssh babel "cd $WDIR; clustalx $temp_file_name.processed"
else
clustalx $temp_file_name.processed clustalx $temp_file_name.processed
fi
exit 0 exit 0
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