Mercurial > repos > geert-vandeweyer > vcf_to_variantdb

changeset 8:db44ff975de8 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Corrected macro.xml handling of GALAXY_URL
author geert-vandeweyer
date Tue, 10 Jun 2014 06:01:18 -0400
parents 04e3bba317f4
children 3b27cae9b359
files VCF_to_VariantDB.pl VCF_to_VariantDB.xml VCF_to_VariantDB_macros.xml
diffstat 3 files changed, 5 insertions(+), 2 deletions(-) [+]
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");
 }	
--- a/VCF_to_VariantDB.xml	Thu Jun 05 04:02:28 2014 -0400
+++ b/VCF_to_VariantDB.xml	Tue Jun 10 06:01:18 2014 -0400
@@ -6,7 +6,7 @@
   </macros>
   <command interpreter="perl">
     VCF_to_VariantDB.pl
-      -H '@URL@'
+      -H "@URL@"
       -R $__root_dir__
       ## input file
       -v $input1
--- a/VCF_to_VariantDB_macros.xml	Thu Jun 05 04:02:28 2014 -0400
+++ b/VCF_to_VariantDB_macros.xml	Tue Jun 10 06:01:18 2014 -0400
@@ -6,6 +6,6 @@
     </requirements>
   </xml>
   <token name="@URL@">
-    $GALAXY_URL/
+    \$GALAXY_URL/
   </token>
 </macros>