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Commit 7d3331fc 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@5525 ee4ac58c-ac51-4696-9907-e4b3aa274f04
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with 26 additions and 347 deletions
etc/run_blastp
+ 26
− 347
View file @ 7d3331fc
......@@ -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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