Mercurial > repos > geert-vandeweyer > clusterfast
changeset 17:b9711e16f148 draft
Uploaded
author | geert-vandeweyer |
---|---|
date | Mon, 28 Jul 2014 12:46:11 -0400 |
parents | 4d719572fc9e |
children | 6b9abfbf796a |
files | run_cf0611.pl |
diffstat | 1 files changed, 4 insertions(+), 2 deletions(-) [+] |
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--- a/run_cf0611.pl Mon Jul 28 10:28:08 2014 -0400 +++ b/run_cf0611.pl Mon Jul 28 12:46:11 2014 -0400 @@ -19,6 +19,7 @@ use File::Path qw(make_path); use Cwd ; use Cwd 'abs_path'; +use File::Basename; my ($inbam, $outdir, $targets, $minct1, $minct2, $dist, $novoindex, $rmtmp, $FASTA,$twobit,$refpaths,$bp1,$bp2,$contigs); @@ -33,9 +34,10 @@ my $scriptspath = ''; my $cffile = ''; # Galaxy installer puts scripts and jar into a folder, which is available under the environment variable CF_PATH +# this is future work (once github of clusterfast gets updated. For now, it's a placeholder. if (defined($ENV{'CF_PATH'}) && -d $ENV{'CF_PATH'}) { - $scriptspath = $ENV{'CF_PATH'}."/cf_scripts"; - $cffile = $ENV{'CF_PATH'}."/cf_v1.1.jar"; + $scriptspath = dirname(abs_path($0))."/cf_scripts"; + $cffile = dirname(abs_path($0))."/cf_v1.1.jar"; } else { $scriptspath="$cwd/cf_scripts";