Mercurial > repos > stef > falco

changeset 12:dc5e86a40851 draft

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Uploaded
author stef
date Wed, 08 Oct 2014 07:15:37 -0400
parents 63f621915e89
children 6d8144665015
files falco.xml
diffstat 1 files changed, 4 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/falco.xml	Wed Oct 08 07:05:41 2014 -0400
+++ b/falco.xml	Wed Oct 08 07:15:37 2014 -0400
@@ -28,7 +28,8 @@
   <!-- command block to call script with default R environment -->
   <command interpreter="bash">
     <!--falco.sh $bam $bam.name $html_output $vcf_output ${html_output.files_path} &amp;&amp;; echo "ECHO PRINT"; -->
-    falco.sh $falco_cfg \$JAVA_JAR_PATH;
+    <!-- falco.sh $falco_cfg \$JAVA_JAR_PATH \$SNPEFF_JAR_PATH; -->
+    falco.sh $falco_cfg;
   </command>
   <!--
   <command interpreter="bash">
@@ -77,6 +78,8 @@
       html_out=$html_output
       vcf_out=$vcf_output
       out_path=${html_output.files_path}
+      jar_path1=\$JAVA_JAR_PATH
+      jar_path2=\$SNPEFF_JAR_PATH
     </configfile>
   </configfiles>