Mercurial > repos > geert-vandeweyer > clusterfast
changeset 26:9f96e2fa94ed draft
Create local tmp folder under /tmp instead of in galaxy_new_file_path location
| author | geert-vandeweyer |
|---|---|
| date | Mon, 11 Aug 2014 05:22:08 -0400 |
| parents | 89f22d2a9dfe |
| children | 4ed740a1f9d9 |
| files | run_cf0611.pl |
| diffstat | 1 files changed, 9 insertions(+), 1 deletions(-) [+] |
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--- 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);