1,102
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to search→Script
=head1 SYNOPSIS
=head1 SYNOPSIS
generate_simple_stuff_makefile [options]
generate_simple_stuff_makefile [options]
-o output directory : location of all output files
-o output directory : location of all output files
-m output make file
-m output make file
example: ./generate_simple_stuff_makefile.pl
example: ./generate_simple_stuff_makefile.pl
=head1 DESCRIPTION
=head1 DESCRIPTION
=cut
=cut
my $outputDir = getcwd();
my $outputDir = getcwd();
my $makeFile = "simple_stuff.mk";
my $makeFile = "simple_stuff.mk";
my $launchMethod = "local";
#initialize options
#initialize options
if(!GetOptions ('h'=>\$help, 'v'=>\$verbose, 'd'=>\$debug,
if(!GetOptions ('h'=>\$help, 'v'=>\$verbose, 'd'=>\$debug,
'o:s'=>\$outputDir,
'o:s'=>\$outputDir,
'm:s'=>\$makeFile)
'l:s'=>\$launchMethod,
|| !defined($outputDir)
'm:s'=>\$makeFile)
|| !defined($outputDir)
|| scalar(@ARGV)!=0)
|| scalar(@ARGV)!=0)
{
{
pod2usage(1);
pod2usage(1);
}
}
}
if ($launchMethod ne "local" && $launchMethod ne "slurm")
{
print STDERR "Launch method has to be local or slurm\n";
exit(1);
}
}
printf("\n");
printf("\n");
printf("output directory : %s\n", $outputDir);
printf("output directory : %s\n", $outputDir);
printf("launch method : %s\n", $launchMethod);
printf("\n");
printf("\n");
$dep = "";
$dep = "";
@cmd = ("echo $i > $outputDir/$i.log");
@cmd = ("echo $i > $outputDir/$i.log");
makeJob($launchMethod, $tgt, $dep, @cmd);
}
}
$dep = $inputFilesOK;
$dep = $inputFilesOK;
@cmd = ("cat $inputFiles > $outputFile");
@cmd = ("cat $inputFiles > $outputFile");
makeJob($launchMethod, $tgt, $dep, @cmd);
###########################
###########################
#3. Cleanup temporary files
#3. Cleanup temporary files
$dep = "$outputDir/all.log.OK";
$dep = "$outputDir/all.log.OK";
@cmd = ("rm $inputFiles");
@cmd = ("rm $inputFiles");
makeJob($launchMethod, $tgt, $dep, @cmd);
#*******************
#*******************
#Write out make file
#Write out make file
#functions
#functions
##########
##########
#run a job either locally or by slurm
sub makeJob
{
my ($method, $tgt, $dep, @cmd) = @_;
if ($method eq "local")
{
makeLocalStep($tgt, $dep, @cmd);
}
elsif ($method eq "slurm")
{
makeSlurm($tgt, $dep, @cmd);
}
}
#run slurm jobs
#run slurm jobs
sub makeSlurm
sub makeSlurm
{
{
my ($tgt, $dep, @cmd) = @_;
my ($tgt, $dep, @cmd) = @_;
