From bfa1b8b645b1cb997cdf763c3b614aa7552c3c09 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 22 Jun 2004 10:39:58 +0000
Subject: [PATCH] set to multi thread and send to different queues depending on
seq length
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@1676 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
etc/run_fasta | 24 +++++++++++++++++++-----
1 file changed, 19 insertions(+), 5 deletions(-)
diff --git a/etc/run_fasta b/etc/run_fasta
index 607a03a6c..4ce1faebc 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 1.2 2004-06-11 14:54:05 tjc Exp $"
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_fasta,v 1.3 2004-06-22 10:39:58 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
@@ -39,11 +39,13 @@ run_one_prog () {
OUTPUT_FILE=$2
DATABASE=$3
-
### change these lines:
+ ### get sequence size
+ seq_size=`infoseq "$INPUT_FILE" -length -only -auto | awk '{ sum += $1 } END { print sum }`
+
FASTLIBS=/nfs/disk222/yeastpub/bio-soft/fasta/pubseqgbs export FASTLIBS
- EXEC=/nfs/disk222/yeastpub/bio-soft/fasta/fasta33
+ EXEC=/nfs/disk222/yeastpub/bio-soft/fasta/fasta33_t
echo "about to start $EXEC with input from $INPUT_FILE and output to" 1>&2
echo "$OUTPUT_FILE using database $DATABASE" 1>&2
@@ -54,8 +56,20 @@ run_one_prog () {
echo "command line: $COMMAND" 1>&2
# lsrun -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -v $COMMAND 2>&1 > $OUTPUT_FILE |
- bsub -q babelq2 -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -I $COMMAND 2>&1 > $OUTPUT_FILE |
- tee ${PROG}_errors.new 1>&2
+
+ if [ "$seq_size" -lt 25000 ]
+ then
+ bsub -q babelq2 -n 1 -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -I $COMMAND 2>&1 > $OUTPUT_FILE |
+ tee ${PROG}_errors.new 1>&2
+ elif [ "$seq_size" -lt 70000 ]
+ then
+ bsub -q "longblastq" -n 1 -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -I $COMMAND 2>&1 > $OUTPUT_FILE |
+ tee ${PROG}_errors.new 1>&2
+ else
+ bsub -q "local_blastq" -n 1 -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -I $COMMAND 2>&1 > $O
+UTPUT_FILE |
+ tee ${PROG}_errors.new 1>&2
+ fi
#### end of changes
--
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