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Commit b19c162e authored by tjc's avatar tjc
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generic version 

git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@2323 ee4ac58c-ac51-4696-9907-e4b3aa274f04
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etc/run_blastn
+ 4
− 25
View file @ b19c162e
......@@ -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 ${PROG}_errors.new 1>&2
#### end of changes
......
etc/run_blastp
+ 5
− 23
View file @ b19c162e
......@@ -6,7 +6,7 @@
# to customise this script see the function called run_one_prog below
RCS_HEADER="$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 $EXPANDED_DATABASE
done
else
......
etc/run_blastx
+ 4
− 25
View file @ b19c162e
......@@ -6,7 +6,7 @@
# to customise this script see the function called run_one_prog below
RCS_HEADER="$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 ${PROG}_errors.new 1>&2
#### end of changes
......
etc/run_clustalx
+ 3
− 21
View file @ b19c162e
......@@ -4,7 +4,7 @@
# contents of files listed in a file of filenames
RCS_HEADER="$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 $temp_file_name.processed
exit 0
etc/run_fasta
+ 11
− 121
View file @ b19c162e
......@@ -6,7 +6,7 @@
# to customise this script see the function called run_one_prog below
RCS_HEADER="$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 $EXPANDED_DATABASE
fi
......
etc/run_fastx
+ 5
− 19
View file @ b19c162e
......@@ -6,7 +6,7 @@
# to customise this script see the function called run_one_prog below
RCS_HEADER="$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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