Mercurial > repos > geert-vandeweyer > vcf_to_variantdb

diff VCF_to_VariantDB.pl @ 8:db44ff975de8 draft

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Corrected macro.xml handling of GALAXY_URL
author geert-vandeweyer
date Tue, 10 Jun 2014 06:01:18 -0400
parents 04e3bba317f4
children 3b27cae9b359
line wrap: on
line diff
--- a/VCF_to_VariantDB.pl	Thu Jun 05 04:02:28 2014 -0400
+++ b/VCF_to_VariantDB.pl	Tue Jun 10 06:01:18 2014 -0400
@@ -111,10 +111,13 @@
 
 ## link files
 $vcfurl = "$dd/data.vcf";
+$vcfurl =~ s/\s//g;
 system ("ln -s $vcfpath $wd/data.vcf");
 if (exists($opts{'b'})) {
 	$bamurl = "$dd/data.bam";
+	$bamurl =~ s/\s//g;
 	$bamidxurl = "$dd/data.bai";
+	$bamidxurl =~ s/\s//g;
 	system ("ln -s $bampath $wd/data.bam");
 	system ("ln -s $baipath $wd/data.bai");
 }