comparison run_cf0611.pl @ 26:9f96e2fa94ed draft

Create local tmp folder under /tmp instead of in galaxy_new_file_path location

25:89f22d2a9dfe

# if refpaths is defined => split into seperate variables.
if (defined($refpaths) && $refpaths ne '') {
	($novoindex, $twobit, $FASTA) = split(/;/,$refpaths);
}

if(! ( defined $inbam && defined $targets && defined $FASTA && defined $outdir && defined $novoindex && defined $twobit )) {
	print STDERR "Usage:  run_cf_0611.pl -b inbam -o outdir -f fasta -t targets  -d distance -i novoindex -r rmtmp -m1 min_pairs -m2 min_splits -t genome.2bit\n";
	exit(1);
}
elsif (! (-e $inbam && -e $targets && -e $FASTA && -e $novoindex && -e $twobit)) {
	print STDERR "Critical file missing.\n";
	exit(1);
}

make_empty_output();
$outdir = abs_path($outdir);

## convert Targets.bed to targets.picard
my $cmd="${SAMTOOLS}samtools view -H $inbam > $outdir/Targets.picard";

26:9f96e2fa94ed

# if refpaths is defined => split into seperate variables.
if (defined($refpaths) && $refpaths ne '') {
	($novoindex, $twobit, $FASTA) = split(/;/,$refpaths);
}

if(! ( defined $inbam && defined $targets && defined $FASTA && defined $novoindex && defined $twobit )) {
	print STDERR "Usage:  run_cf_0611.pl -b inbam -o outdir -f fasta -t targets  -d distance -i novoindex -r rmtmp -m1 min_pairs -m2 min_splits -t genome.2bit\n";
	exit(1);
}
elsif (! (-e $inbam && -e $targets && -e $FASTA && -e $novoindex && -e $twobit)) {
	print STDERR "Critical file missing.\n";
	exit(1);
}

# output dir specified?
if (!defined($outdir)) {
	$outdir = "/tmp/cf_tmp_".int(rand(1000));
	while (-d $outdir) {
		$outdir = "/tmp/cf_tmp_".int(rand(1000));
	}
}
# prepare output dir
make_empty_output();
$outdir = abs_path($outdir);

## convert Targets.bed to targets.picard
my $cmd="${SAMTOOLS}samtools view -H $inbam > $outdir/Targets.picard";