From 8b7f336e8af5392a91f8b9ae1dfc1983ecc7d1c5 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 5 Oct 2004 12:40:05 +0000
Subject: [PATCH] change to be able to run on deskpro
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@1913 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
etc/run_blastp | 29 +++++++++++++++++++++++------
etc/run_fasta | 24 ++++++++++++++++++++----
2 files changed, 43 insertions(+), 10 deletions(-)
diff --git a/etc/run_blastp b/etc/run_blastp
index 2ac573c1b..95a98a318 100755
--- a/etc/run_blastp
+++ b/etc/run_blastp
@@ -6,7 +6,7 @@
# to customise this script see the function called run_one_prog below
-RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastp,v 1.1 2004-06-09 10:02:59 tjc Exp $"
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastp,v 1.2 2004-10-05 12:40:05 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
@@ -49,11 +49,28 @@ run_one_prog () {
EXTRA_ARGS=
+ HOSTNAME=`hostname`
+ REMOTE=N
+
+ case $HOSTNAME in
+ deskpro*)
+ REMOTE=Y ;;
+ *)
+ esac
+
+ if [ $REMOTE = "Y" ]; then
+ WDIR=`pwd`
+ export WDIR
+ rsh babel "cd $WDIR; lsrun -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -v \
+ blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastp \
+ $EXTRA_ARGS >! $OUTPUT_FILE"
+ else
# add/change the flags to suit your site:
- lsrun -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -v \
- blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastp \
- $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
- tee ${PROG}_errors.new 1>&2
+ lsrun -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -v \
+ blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastp \
+ $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
+ tee ${PROG}_errors.new 1>&2
+ fi
#### end of changes
@@ -78,7 +95,7 @@ if [ x$ONEFILE = x ]
then
for i in `cat $1`
do
- run_one_prog $i $i.out $EXPANDED_DATABASE
+ run_one_prog $i $i.out $EXPANDED_DATABASE
done
else
diff --git a/etc/run_fasta b/etc/run_fasta
index 50927e9de..d11e66936 100755
--- a/etc/run_fasta
+++ b/etc/run_fasta
@@ -6,7 +6,7 @@
# to customise this script see the function called run_one_prog below
-RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_fasta,v 1.8 2004-07-21 15:16:45 tjc Exp $"
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_fasta,v 1.9 2004-10-05 12:39:52 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
@@ -145,11 +145,11 @@ while(my $inFile = <LIST_FILE>)
$inFile = $inFile_tmp;
}
}
-
+
print BSUB "$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 BSUB or die "--Could not submit job : $!";
close LIST_FILE;
'
@@ -158,9 +158,25 @@ close LIST_FILE;
chmod a+x $PROG.kill
+HOSTNAME=`hostname`
+REMOTE=N
+
+case $HOSTNAME in
+ deskpro*)
+ REMOTE=Y ;;
+ *)
+esac
+
if [ x$ONEFILE = x ]
then
- perl -w -e "$PERL_PROG" "$1" "$EXPANDED_DATABASE" "$PWD"
+ if [ $REMOTE = "Y" ]; then
+ WDIR=`pwd`
+ export WDIR
+ CMD=`echo $PERL_PROG`
+ rsh babel "cd $WDIR; perl -w -e '$CMD' \"$1\" \"$EXPANDED_DATABASE\" \"$PWD\""
+ else
+ perl -w -e "$PERL_PROG" "$1" "$EXPANDED_DATABASE" "$PWD"
+ fi
else
run_one_prog $1 $2 $EXPANDED_DATABASE
fi
--
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