# HG changeset patch
# User geert-vandeweyer
# Date 1407748928 14400
# Node ID 9f96e2fa94ed24bd1a2fc9b0d9a054295b57c26c
# Parent  89f22d2a9dfe924beea014d6a7fe356ed9ae83cf
Create local tmp folder under /tmp instead of in galaxy_new_file_path location

diff -r 89f22d2a9dfe -r 9f96e2fa94ed run_cf0611.pl
--- a/run_cf0611.pl	Mon Aug 11 05:21:21 2014 -0400
+++ b/run_cf0611.pl	Mon Aug 11 05:22:08 2014 -0400
@@ -97,7 +97,7 @@
 	($novoindex, $twobit, $FASTA) = split(/;/,$refpaths);
 }
 
-if(! ( defined $inbam && defined $targets && defined $FASTA && defined $outdir && defined $novoindex && defined $twobit )) {
+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);
 }
@@ -106,6 +106,14 @@
 	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);