From b19c162e20dfc02467db28b7449d1e14417e0c99 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Mon, 21 Feb 2005 11:54:10 +0000
Subject: [PATCH] generic version
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2323 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
etc/run_blastn | 29 ++---------
etc/run_blastp | 28 ++--------
etc/run_blastx | 29 ++---------
etc/run_clustalx | 24 ++-------
etc/run_fasta | 132 ++++-------------------------------------------
etc/run_fastx | 24 ++-------
6 files changed, 32 insertions(+), 234 deletions(-)
diff --git a/etc/run_blastn b/etc/run_blastn
index fdcaa65a6..513ff047a 100755
--- a/etc/run_blastn
+++ b/etc/run_blastn
@@ -6,7 +6,7 @@
# to customise this script see the function called run_one_prog below
-RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastn,v 1.2 2004-10-05 13:59:39 tjc Exp $"
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastn,v 1.3 2005-02-21 11:42:46 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
@@ -50,30 +50,9 @@ run_one_prog () {
EXTRA_ARGS=
# add/change the flags to suit your site:
-
- HOSTNAME=`hostname`
- REMOTE=N
-
- case $HOSTNAME in
- deskpro*)
- REMOTE=Y ;;
- *)
- esac
-
- if [ $REMOTE = "Y" ]; then
- WDIR=`pwd`
- export WDIR
- rsh babel "cd $WDIR; lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastn \
- $EXTRA_ARGS >! $OUTPUT_FILE"
- else
- lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastn \
- $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
- tee ${PROG}_errors.new 1>&2
- fi
-
-# lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastn \
-# $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
-# tee ${PROG}_errors.new 1>&2
+ nice -19 $EXEC -d $DATABASE -i $INPUT_FILE -p blastn \
+ $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
+ tee ${PROG}_errors.new 1>&2
#### end of changes
diff --git a/etc/run_blastp b/etc/run_blastp
index 95a98a318..853a249d3 100755
--- a/etc/run_blastp
+++ b/etc/run_blastp
@@ -6,7 +6,7 @@
# to customise this script see the function called run_one_prog below
-RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastp,v 1.2 2004-10-05 12:40:05 tjc Exp $"
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastp,v 1.3 2005-02-21 11:45:33 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
@@ -49,28 +49,10 @@ 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
- fi
+ nice -19 $EXEC -d $DATABASE -i $INPUT_FILE -p blastp \
+ $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
+ tee ${PROG}_errors.new 1>&2
#### end of changes
@@ -95,7 +77,7 @@ if [ x$ONEFILE = x ]
then
for i in `cat $1`
do
- run_one_prog $i $i.out $EXPANDED_DATABASE
+ run_one_prog $i $i.out $EXPANDED_DATABASE
done
else
diff --git a/etc/run_blastx b/etc/run_blastx
index 700f09f3b..4172bfbad 100755
--- a/etc/run_blastx
+++ b/etc/run_blastx
@@ -6,7 +6,7 @@
# to customise this script see the function called run_one_prog below
-RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastx,v 1.2 2004-10-05 14:53:49 tjc Exp $"
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastx,v 1.3 2005-02-21 11:46:53 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
@@ -50,30 +50,9 @@ run_one_prog () {
EXTRA_ARGS=
# add/change the flags to suit your site:
-
- HOSTNAME=`hostname`
- REMOTE=N
-
- case $HOSTNAME in
- deskpro*)
- REMOTE=Y ;;
- *)
- esac
-
- if [ $REMOTE = "Y" ]; then
- WDIR=`pwd`
- export WDIR
- rsh babel "cd $WDIR; lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastx \
- $EXTRA_ARGS >! $OUTPUT_FILE"
- else
- lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastx \
- $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
- tee ${PROG}_errors.new 1>&2
- fi
-
-# lsrun -v blastwrap.pl $EXEC -d $DATABASE -i $INPUT_FILE -p blastx \
-# $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
-# tee ${PROG}_errors.new 1>&2
+ nice -19 $EXEC -d $DATABASE -i $INPUT_FILE -p blastx \
+ $EXTRA_ARGS 2>&1 > $OUTPUT_FILE |
+ tee ${PROG}_errors.new 1>&2
#### end of changes
diff --git a/etc/run_clustalx b/etc/run_clustalx
index f7b5a603a..0b9dd6a12 100755
--- a/etc/run_clustalx
+++ b/etc/run_clustalx
@@ -4,7 +4,7 @@
# contents of files listed in a file of filenames
-RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_clustalx,v 1.2 2004-10-05 15:21:47 tjc Exp $"
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_clustalx,v 1.3 2005-02-21 11:50:01 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
@@ -21,7 +21,7 @@ chmod a+x $PROG.kill
file_of_filenames=$1
date=`date +"%y_%m_%d"`
hostname=`hostname`
-temp_file_name=clustalx/artemis_temp.$$.$hostname.$date.clustalx_input.fasta
+temp_file_name=/tmp/artemis_temp.$$.$hostname.$date.clustalx_input.fasta
cat $file_of_filenames | xargs cat > $temp_file_name
@@ -36,24 +36,6 @@ perl -pne 'if (/^>(\S+)/) {
}
}' $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
-fi
+clustalx $temp_file_name.processed
exit 0
diff --git a/etc/run_fasta b/etc/run_fasta
index 6e4f9b95c..31147c37b 100755
--- a/etc/run_fasta
+++ b/etc/run_fasta
@@ -6,7 +6,7 @@
# to customise this script see the function called run_one_prog below
-RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_fasta,v 1.11 2005-01-14 14:24:40 tjc Exp $"
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_fasta,v 1.12 2005-02-21 11:51:32 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
@@ -28,30 +28,10 @@ else
fi
-#
-# Exchange DB name for fasta reference
-#
-if [ "$DATABASE" = "%uniprot" ]; then
- DATABASE="%U";
-elif [ "$DATABASE" = "%uniprot_archaea" ]; then
- DATABASE="%A";
-elif [ "$DATABASE" = "%uniprot_bacteria" ]; then
- DATABASE="%B";
-elif [ "$DATABASE" = "%uniprot_eukaryota" ]; then
- DATABASE="%E";
-elif [ "$DATABASE" = "%uniprot_viruses" ]; then
- DATABASE="%V";
-elif [ "$DATABASE" = "%uniprot_rest" ]; then
- DATABASE="%R";
-elif [ "$DATABASE" = "%malaria" ]; then
- DATABASE="%M";
-elif [ "$DATABASE" = "%kineto_aa" ]; then
- DATABASE="%K";
-fi
-
# expand any ~ or environment variables
EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
+
### change this function to suit your site:
run_one_prog () {
@@ -59,41 +39,21 @@ run_one_prog () {
OUTPUT_FILE=$2
DATABASE=$3
-### strip out directory from command line
- IN=`echo $INPUT_FILE | sed -n -e "s|$PWD//||p"`
-
- if test "$IN" != "" && test -f $IN; then
- INPUT_FILE="$IN"
- fi
-
- echo "\n\nIN=$IN\nPWD=$PWD\nINPUT_FILE=$INPUT_FILE\n\n"
### change these lines:
- ### get sequence size
- seq_size=`infoseq "$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_t
+ EXEC=fasta34
echo "about to start $EXEC with input from $INPUT_FILE and output to" 1>&2
echo "$OUTPUT_FILE using database $DATABASE" 1>&2
# add/change the flags to suit your site:
- COMMAND="$EXEC -B -S -q -b 100 -H $INPUT_FILE $DATABASE ktup 2"
+ COMMAND="$EXEC -B -S -q -b 40 -H $INPUT_FILE $DATABASE ktup 2"
echo "command line: $COMMAND" 1>&2
-# lsrun -R 'select[blast && mem > 500] rusage[r1m=1:mem=500]' -v $COMMAND 2>&1 > $OUTPUT_FILE |
-
- if [ "$seq_size" -lt 50000 ]
- then
- bsub -q normal -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 "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
- fi
+ nice -19 $COMMAND 2>&1 > $OUTPUT_FILE |
+ tee ${PROG}_errors.new 1>&2
#### end of changes
@@ -110,87 +70,17 @@ run_one_prog () {
fi
}
-PERL_PROG='
-
-local *BSUB;
-
-my $file = $ARGV[0];
-my $database = $ARGV[1];
-my $pwd = $ARGV[2];
-chomp $file;
-chomp $database;
-
-$ENV{'FASTLIBS'} = "/nfs/disk222/yeastpub/bio-soft/fasta/pubseqgbs_test";
-
-
-open(BSUB, "| bsub -q normal -o fasta_errors -n 1 -R \"select[blast && mem > 500] rusage[r1m=1:mem=500]\" -K") or die "could not open bsub pipe : $!";
-open(LIST_FILE,$file);
-
-$EXEC="/nfs/disk222/yeastpub/bio-soft/fasta/fasta33_t";
-
-while(my $inFile = <LIST_FILE>)
-{
- chomp($inFile);
-
- if($inFile =~ m/^($pwd)(.*)/)
- {
- my $inFile_tmp = $2;
- while($inFile_tmp =~ m/^(\/)(.*)/)
- {
- $inFile_tmp = $2;
- }
-
- if( -e $inFile_tmp )
- {
- $inFile = $inFile_tmp;
- }
- }
-
- if($inFile =~ m/^(\S{100})/)
- {
- if($inFile =~ m/^(\S{90,})(fasta\/\S+)/)
- {
- my $inFile_tmp = $1;
-
- if( -e $inFile_tmp )
- {
- print BSUB "cd $inFile_tmp\n";
- $inFile = $2;
- }
- }
- }
-
- print BSUB "$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 LIST_FILE;
-
-'
-
(echo "#!/bin/sh -"; echo "kill $$") > $PROG.kill
chmod a+x $PROG.kill
-HOSTNAME=`hostname`
-REMOTE=N
-
-case $HOSTNAME in
- deskpro*)
- REMOTE=Y ;;
- *)
-esac
-
if [ x$ONEFILE = x ]
then
- 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
+ for i in `cat $1`
+ do
+ run_one_prog $i $i.out $EXPANDED_DATABASE
+ done
+
else
run_one_prog $1 $2 $EXPANDED_DATABASE
fi
diff --git a/etc/run_fastx b/etc/run_fastx
index 833c89690..e37d4b4cd 100644
--- a/etc/run_fastx
+++ b/etc/run_fastx
@@ -6,7 +6,7 @@
# to customise this script see the function called run_one_prog below
-RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_fastx,v 1.2 2004-10-05 15:43:08 tjc Exp $"
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_fastx,v 1.3 2005-02-21 11:54:10 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
@@ -49,26 +49,12 @@ run_one_prog () {
echo "$OUTPUT_FILE using database $DATABASE" 1>&2
# add/change the flags to suit your site:
- HOSTNAME=`hostname`
- REMOTE=N
-
- case $HOSTNAME in
- deskpro*)
- REMOTE=Y ;;
- *)
- esac
-
COMMAND="$EXEC -B -S -q -b 40 -H $INPUT_FILE $DATABASE ktup 2"
- echo "command line: $COMMAND" 1>&2
- if [ $REMOTE = "Y" ]; then
- WDIR=`pwd`
- export WDIR
- rsh babel "cd $WDIR; $COMMAND >! $OUTPUT_FILE"
- else
- $COMMAND 2>&1 > $OUTPUT_FILE |
- tee ${PROG}_errors.new 1>&2
- fi
+ echo "command line: $COMMAND" 1>&2
+
+ $COMMAND 2>&1 > $OUTPUT_FILE |
+ tee ${PROG}_errors.new 1>&2
#### end of changes
--
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