From 7d3331fca595e9e101e84578267047a0074828a1 Mon Sep 17 00:00:00 2001
From: tjc <tjc@ee4ac58c-ac51-4696-9907-e4b3aa274f04>
Date: Tue, 27 Feb 2007 10:59:41 +0000
Subject: [PATCH] generic version
git-svn-id: svn+ssh://svn.internal.sanger.ac.uk/repos/svn/pathsoft/artemis/trunk@5525 ee4ac58c-ac51-4696-9907-e4b3aa274f04
---
etc/run_blastp | 373 ++++---------------------------------------------
1 file changed, 26 insertions(+), 347 deletions(-)
diff --git a/etc/run_blastp b/etc/run_blastp
index 2ee1b2a1b..6edeae90d 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 1.5 2006-06-21 10:11:36 tjc Exp $"
+RCS_HEADER="$Header: //tmp/pathsoft/artemis/etc/run_blastp,v 1.6 2007-02-27 10:59:41 tjc Exp $"
PROG=`echo $RCS_HEADER | sed 's/.*run_\(.*\),v.*/\1/'`
@@ -21,17 +21,17 @@ else
then
DATABASE=$2 export DATABASE
else
- echo usage: $0 -onefile input_file output_file database 1>&2
- echo or: $0 file_of_filenames database 1>&2
+ echo usage: $0 -onefile input_file output_file database
+ echo or: $0 file_of_filenames database
exit 1
fi
fi
-
# expand any ~ or environment variables
EXPANDED_DATABASE=`echo "echo $DATABASE" | /bin/csh -f`
+
### change this function to suit your site:
run_one_prog () {
@@ -41,7 +41,19 @@ run_one_prog () {
### change these lines:
- EXEC=blastall
+ EXEC=${EXEC-`which blastall 2>/dev/null`}
+
+ if [ ! -x "$EXEC" ]; then
+ EXEC=`find Artemis* -name blastall 2>/dev/null`
+ fi
+
+ if [ ! -d "$BLASTDB" ]; then
+ DATABASE_TMP=`echo $DATABASE | sed 's|\%||'`
+ DATABASE_TMP="$PWD/"`find Artemis* -name blast-data 2>/dev/null`"/$DATABASE_TMP"
+ if [ -f "$DATABASE_TMP" ]; then
+ DATABASE="$DATABASE_TMP"
+ fi
+ fi
echo "about to start $EXEC with input from $INPUT_FILE and output to"
echo "$OUTPUT_FILE using database $DATABASE"
@@ -49,30 +61,10 @@ 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"
- ssh babel "cd $WDIR; bsub -q longblastq -o $OUTPUT_FILE -e ${PROG}_errors.new -I flexi_blast.pl -p $DATABASE $INPUT_FILE $EXTRA_ARGS"
- 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
- bsub -q longblastq -o $OUTPUT_FILE -e ${PROG}_errors.new -I flexi_blast.pl -p $DATABASE $INPUT_FILE $EXTRA_ARGS
- 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
@@ -82,337 +74,24 @@ run_one_prog () {
if [ -s ${PROG}_errors.new ]
then
- ( echo ERROR running $PROG: ; echo;
+ ( echo ERROR running $PROG: ; echo;
echo ===================================================
cat ${PROG}_errors.new ) >> $OUTPUT_FILE
cat ${PROG}_errors.new >> ${PROG}_errors
fi
}
-PERL_PROG_1='
-
-local *BSUB;
-
-my $file = $ARGV[0];
-my $database = $ARGV[1];
-my $pwd = $ARGV[2];
-chomp $file;
-chomp $database;
-
-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="blastall";
-
-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,})(blastp\/\S+)/)
- {
- my $inFile_tmp = $1;
-
- if( -e $inFile_tmp )
- {
- print BSUB "cd $inFile_tmp\n";
- $inFile = $2;
- }
- }
- }
-
- print BSUB "flexi_blast.pl -p $database $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;
-'
-
-
-
-PERL_PROG='
-
-local *BSUB;
-
-my $file = $ARGV[0];
-my $database = $ARGV[1];
-my $pwd = $ARGV[2];
-chomp $file;
-chomp $database;
-
-open(LIST_FILE,$file);
-
-$NEW_WDIR=".";
-$NUM_JOBS=0;
-
-while(my $inFile = <LIST_FILE>)
-{
- $NUM_JOBS++;
- chomp($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,})(blastp\/\S+)/)
- {
- my $inFile_tmp = $1;
-
- if( -e $inFile_tmp )
- {
- $NEW_WDIR=$inFile_tmp;
- $inFile = $2;
- }
- }
- }
- # find number of leading zero
-
- if($inFile =~ m/^(.*)(blastp\/)([^\/]*)(0{4})(\d{1})$/)
- {
- push(@jobs10, $inFile);
- }
- elsif($inFile =~ m/^(.*)(blastp\/)([^\/]*)(0{3})(\d{2})$/)
- {
- push(@jobs100, $inFile);
- }
- elsif($inFile =~ m/^(.*)(blastp\/)([^\/]*)(0{2})(\d{3})$/)
- {
- push(@jobs1000, $inFile);
- }
- elsif($inFile =~ m/^(.*)(blastp\/)([^\/]*)(0{1})(\d{4})$/)
- {
- push(@jobs10000, $inFile);
- }
- else
- {
- push(@jobs100000, $inFile);
- }
-}
-close LIST_FILE;
-
-if(defined @jobs10)
-{
- my( $num ) = sprintf( "%04d", 0);
- submit($num, @jobs10);
-}
-
-if(defined @jobs100)
-{
- my( $num ) = sprintf( "%03d", 0);
- submit($num, @jobs100);
-}
-
-if(defined @jobs1000)
-{
- my( $num ) = sprintf( "%02d", 0);
- submit($num, @jobs1000);
-}
-
-if(defined @jobs10000)
-{
- my( $num ) = sprintf( "%01d", 0);
- submit($num, @jobs10000);
-}
-
-if(defined @jobs100000)
-{
- submit("", @jobs100000);
-}
-
-for($count = 0; $count < @bsub_jobs; $count++)
-{
- open(BSUB, "| bsub -q normal -R \"select[mem > 1] rusage[mem=1]\" -o /dev/null -e /dev/null -w \"ended($bsub_jobs[$count])\" -K -J \"$bsub_jobs[$count]\_fin\"") or die "could not open bsub pipe : $!";
- print BSUB "\"echo finished > /dev/null\" > /dev/null 2> /dev/null";
- close BSUB; # or die "--Could not submit job : $!";
-}
-
-
-sub submit
-{
- my ($num, @jobs) = @_;
-
- my $prefix;
- my @starts;
- my @prefixes;
-
- if($jobs[0] =~ m/^(.*)(\/blastp\/)([^\/]*)(\d{5})/)
- {
- $prefix = $1.$2.$3;
- push(@starts, "$4");
- }
- elsif($jobs[0] =~ m/^(blastp\/)([^\/]*)(\d{5})/)
- {
- $prefix = $1.$2;
- push(@starts, "$3");
- }
-
- # escape characters
- if($prefix =~ /(\+|\?|\*|\[|\])/)
- {
- $prefix =~ s/\+/\\+/;
- $prefix =~ s/\?/\\?/;
- $prefix =~ s/\*/\\*/;
- $prefix =~ s/\[/\\[/;
- $prefix =~ s/\]/\\]/;
- }
- push(@prefixes, $prefix);
-
-
- #different entries have different prefixes
- for($count =0; $count < @jobs; $count++)
- {
- if($jobs[$count] !~ m/^$prefix(.*)/)
- {
- if($jobs[$count] =~ m/^(.*)(blastp\/)([^\/]*)(\d{5})/)
- {
- $prefix = $1.$2.$3;
-
- push(@starts, "$4");
-
- if($prefix =~ /(\+|\?|\*|\[|\])/)
- {
- $prefix =~ s/\+/\\+/;
- $prefix =~ s/\?/\\?/;
- $prefix =~ s/\*/\\*/;
- $prefix =~ s/\[/\\[/;
- $prefix =~ s/\]/\\]/;
- }
-
- push(@prefixes, $prefix);
- }
- }
- }
-
- for($count =0; $count < @prefixes; $count++)
- {
- $prefix = $prefixes[$count];
- $start = $starts[$count];
-
- # build the index description that need to be run
- $index="$start-";
- $end="$start";
- for($j =0; $j < @jobs; $j++)
- {
- if($jobs[$j] =~ m/^$prefix(.*)/)
- {
- if($jobs[$j] =~ m/^(.*)(blastp\/)([^\/]*)(\d{5})/)
- {
- if($j == @jobs-1)
- {
- $index = "$index$4";
- }
- elsif($end+1 >= $4)
- {
- $end = "$4";
- }
- else
- {
- $index = "$index$end,$4-"
- }
- }
- }
- }
-
- if($index =~ m/(\-)$/)
- {
- $index = "$index$end";
- }
-
- print "$prefix, $index, $num";
- bsub($prefix, $index, $num);
- }
-}
-
-
-# start job arrays
-sub bsub
-{
- my ($prefix, $index, $num) = @_;
-
- my $name = $prefix;
-
- if($prefix =~ m/(\/blastp\/)(.*)/)
- {
- $name = "$2";
- }
-
- my $random = int( rand( 999+1 ) );
-
- push(@bsub_jobs, "$name$random\_blastp");
-
- my $QUEUE="longblastq";
- if($NUM_JOBS <= 6)
- {
- $QUEUE="normal";
- }
-
- print "flexi_blast.pl -p $database $prefix$num\n";
-
- open(BSUB, "| bsub -q $QUEUE -o /dev/null -n 1 -R \"select[blast && mem > 500] rusage[mem=500]\" -J$name$random\_blastp\"[$index]%16\"") or die "could not open bsub pipe : $!";
- print BSUB "cd $NEW_WDIR\n";
- print BSUB "flexi_blast.pl -p $database $prefix$num";
- print BSUB "\${LSB_JOBINDEX} > $prefix$num";
- print BSUB "\${LSB_JOBINDEX}\.out\n";
-
- print BSUB "gzip -9f $prefix$num";
- print BSUB "\${LSB_JOBINDEX}\.out\n";
-
- close BSUB or die "--Could not submit job : $!";
-}
-
-'
-
(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_1`
- ssh 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
--
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