Skip to content
Snippets Groups Projects
Commit 0cc073db authored by tjc's avatar tjc
Browse files

use ssh

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2876 ee4ac58c-ac51-4696-9907-e4b3aa274f04
parent cc8a8453
No related branches found
No related tags found
No related merge requests found
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
# to customise this script see the function called run_one_prog below # to customise this script see the function called run_one_prog below
RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastp.sanger,v 1.2 2005-06-09 13:06:56 tjc Exp $" RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastp.sanger,v 1.3 2005-06-15 19:12:04 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'` PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
...@@ -68,7 +68,7 @@ run_one_prog () { ...@@ -68,7 +68,7 @@ run_one_prog () {
# rsh babel "cd $WDIR; lsrun -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -v \ # 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 \ # blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastp \
# $EXTRA_ARGS >! $OUTPUT_FILE" # $EXTRA_ARGS >! $OUTPUT_FILE"
rsh babel "bsub -q longblastq -o $OUTPUT_FILE -e ${PROG}_errors.new -I flexi_blast.pl -p $DATABASE $INPUT_FILE $EXTRA_ARGS" ssh babel "bsub -q longblastq -o $OUTPUT_FILE -e ${PROG}_errors.new -I flexi_blast.pl -p $DATABASE $INPUT_FILE $EXTRA_ARGS"
else else
# add/change the flags to suit your site: # add/change the flags to suit your site:
# lsrun -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -v \ # lsrun -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -v \
......
...@@ -6,7 +6,7 @@ ...@@ -6,7 +6,7 @@
# to customise this script see the function called run_one_prog below # to customise this script see the function called run_one_prog below
RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_fasta.sanger,v 1.1 2005-02-21 11:51:10 tjc Exp $" RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_fasta.sanger,v 1.2 2005-06-15 19:08:48 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'` PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
...@@ -187,7 +187,7 @@ then ...@@ -187,7 +187,7 @@ then
WDIR=`pwd` WDIR=`pwd`
export WDIR export WDIR
CMD=`echo $PERL_PROG` CMD=`echo $PERL_PROG`
rsh babel "cd $WDIR; perl -w -e '$CMD' \"$1\" \"$EXPANDED_DATABASE\" \"$PWD\"" ssh babel "cd $WDIR; perl -w -e '$CMD' \"$1\" \"$EXPANDED_DATABASE\" \"$PWD\""
else else
perl -w -e "$PERL_PROG" "$1" "$EXPANDED_DATABASE" "$PWD" perl -w -e "$PERL_PROG" "$1" "$EXPANDED_DATABASE" "$PWD"
fi fi
......
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment