From 52f5a584c759b573967bf7718c8be1fd2c0a06dd Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Thu, 9 Jun 2005 13:40:12 +0000
Subject: [PATCH] convert to flexi_blast script
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2805 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
etc/run_tblastx | 14 ++++++++------
1 file changed, 8 insertions(+), 6 deletions(-)
diff --git a/etc/run_tblastx b/etc/run_tblastx
index c2b09bb8f..c6af66b62 100755
--- a/etc/run_tblastx
+++ b/etc/run_tblastx
@@ -6,7 +6,7 @@
# to customise this script see the function called run_one_prog below
-RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_tblastx,v 1.2 2004-10-05 16:01:40 tjc Exp $"
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_tblastx,v 1.3 2005-06-09 13:40:12 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
@@ -62,12 +62,14 @@ run_one_prog () {
if [ $REMOTE = "Y" ]; then
WDIR=`pwd`
export WDIR
- rsh babel "cd $WDIR; lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p tblastx \
- $EXTRA_ARGS >! $OUTPUT_FILE"
+# rsh babel "cd $WDIR; lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p tblastx \
+# $EXTRA_ARGS >! $OUTPUT_FILE"
+ rsh babel "cd $WDIR; bsub -q longblastq -o $OUTPUT_FILE -e ${PROG}_errors.new -I flexi_blast.pl -tx $DATABASE $INPUT_FILE $EXTRA_ARGS"
else
- lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p tblastx \
- $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
- tee ${PROG}_errors.new 1>&2
+# lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p tblastx \
+# $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
+# tee ${PROG}_errors.new 1>&2
+ bsub -q longblastq -o $OUTPUT_FILE -e ${PROG}_errors.new -I flexi_blast.pl -tx $DATABASE $INPUT_FILE $EXTRA_ARGS
fi
#### end of changes
--
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