#!/usr/bin/perl
#
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#   qsub_generate_probes.pl
#
#   Program generates a bash script to run with Sun Grid Engine.
#
#    Designs probes using multi_soop.pl
#
#   Use of Sun Grid Engine allows multiple jobs to be generated
#   by this program and SGE queues them and executes each as
#   machine resources are available.
#
#   Command-line Parameters :
#
#       (1) executables directory - where 'multi_soop.pl' is located
#             e.g.  /home/yourId/sample/bin
#
#
#  Before running this program you must 'cd' into directory where
#  your .maf file and .cfg file are located (see README for Build 2).
#  This directory will also contain all other data files produced
#  during later steps of probe generation process.
#
#  syntax : qsub_generate_probes.pl  /yourExecutablesDirectory
#
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if (@ARGV != 1) {
  die "usage: $0 executableDirectory \n";
}
my $exeDir=$ARGV[0];
#
open (IN,"ls *.maf |") || die "Hey - You dont have any MAF files for me !";
while (<IN>) {
        chop;
        print "Creating file for $_ \n"; 
        ($chromosome) = ($_ =~ m/chr(.+).maf/);
        $maf_file = $_;
        $probefile = "chr".$chromosome.".xml";
        $stdout = "chr".$chromosome.".out";
        my $jobname ="Job_Chromosome_".$chromosome;
        my $outname= "chr".$chromosome. ".bash";
        open(OUT,"> $outname");

        print OUT "#!/bin/bash \n";
        print OUT "#\$ -N $jobname \n";
        print OUT "#\$ -S /bin/bash \n";
        print OUT "#\$ -o $stdout \n";
        print OUT "#\$ -cwd \n";
        print OUT "#\$ -m be \n";
      # print OUT "#\$ -M yourEmailId\@your.email.domain \n";
        print OUT "# \n";
#
#
        print OUT "$exeDir/multi_soop.pl $maf_file -scoring_file score.cfg -species human -probefile $probefile -verbose\n";
        close OUT;
        system("qsub $outname");
}

##############################################################################
# Start Description
# Run multi_soop.pl once for each input file in current directory.
# End Description
##############################################################################