# HG changeset patch
# User niels
# Date 1560172863 14400
# Node ID 0044b989f60f38518d8e51d5d110cb7ffcecb825
# Parent  ce16079341bfb4762f90dbb92067cdabbe2544a8
Uploaded

diff -r ce16079341bf -r 0044b989f60f annovar_yaml/YAML_annovar.yml
diff -r ce16079341bf -r 0044b989f60f annovar_yaml/YAML_arguments_annovar.yml
diff -r ce16079341bf -r 0044b989f60f annovar_yaml/annovar_yaml.pl
--- a/annovar_yaml/annovar_yaml.pl	Mon Jun 10 07:53:19 2019 -0400
+++ b/annovar_yaml/annovar_yaml.pl	Mon Jun 10 09:21:03 2019 -0400
@@ -695,6 +695,16 @@
         print "command3: $command\n";
         system ( $command );
       }
+      if ( $alias =~ /^Annotation$/ ) {
+        my $command = "ln -s $path_folder_symlinks/$species\_$database_detail\Mrna.fa $path_symlinks$species\_$alias\Mrna.fa";
+        print "command4: $command\n";
+        system ( $command );
+      }
+      if ( $database_detail =~ /^clinvar/ ) {
+        my $command = "ln -s $path_folder_symlinks/$species\_$database_detail.txt.idx $path_symlinks$species\_$database_detail.txt.idx";
+        print "command3: $command\n";
+        system ( $command );
+      }
 
       #Push all softlinks used in array
       if ( $alias !~ /^N\/A$/ ) {
diff -r ce16079341bf -r 0044b989f60f annovar_yaml/annovar_yaml.xml
--- a/annovar_yaml/annovar_yaml.xml	Mon Jun 10 07:53:19 2019 -0400
+++ b/annovar_yaml/annovar_yaml.xml	Mon Jun 10 09:21:03 2019 -0400
@@ -7,7 +7,7 @@
         <requirement type="package" version="2.50">perl-getopt-long</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        perl $__tool_directory__/annovar_yaml.pl --paryml /data/annovar/YAML_arguments_annovar.yml --invcf $vcf --inyml $yaml --outvcf $output
+        perl $__tool_directory__/annovar_yaml.pl --invcf $vcf --inyml $yaml --outvcf $output
     ]]></command>
 
     <inputs>