Mercurial > repos > iuc > snpsift_genesets

changeset 2:9ba6e2c298ab draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpsift/snpsift commit 44b3b8a31f9f912a3b754aef1d467a90a4ed3504
author iuc
date Mon, 19 Sep 2016 14:43:55 -0400
parents 0af41de4eda1
children 847db7b39bdc
files snpSift_geneSets.xml snpSift_macros.xml
diffstat 2 files changed, 7 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/snpSift_geneSets.xml	Tue Jun 07 10:05:20 2016 -0400
+++ b/snpSift_geneSets.xml	Mon Sep 19 14:43:55 2016 -0400
@@ -10,6 +10,7 @@
     <expand macro="stdio" />
     <expand macro="version_command" />
     <command><![CDATA[
+        @CONDA_SNPEFF_JAR_PATH@ &&
         java -Xmx2G -jar "\$SNPEFF_JAR_PATH/SnpSift.jar" geneSets -v
         #if $db_opts.db_opts_selector == "db"
           "${db_opts.database.fields.path}"
--- a/snpSift_macros.xml	Tue Jun 07 10:05:20 2016 -0400
+++ b/snpSift_macros.xml	Mon Sep 19 14:43:55 2016 -0400
@@ -10,8 +10,13 @@
         <exit_code range="1:"  level="fatal" description="Error" />
     </stdio>
   </xml>
+  <token name="@CONDA_SNPEFF_JAR_PATH@">if [ -z "\$SNPEFF_JAR_PATH" ]; then export SNPEFF_JAR_PATH=\$(dirname \$(readlink -e \$(which snpEff))); fi</token>
   <xml name="version_command">
-    <version_command>java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version</version_command>
+    <version_command><![CDATA[
+    if [ -z "$SNPEFF_JAR_PATH" ]; then
+        export SNPEFF_JAR_PATH=$(dirname $(readlink -e $(which snpEff)));
+    fi && java -jar "$SNPEFF_JAR_PATH/snpEff.jar" -version
+    ]]></version_command>
   </xml>
   <token name="@WRAPPER_VERSION@">4.1</token>
   <token name="@EXTERNAL_DOCUMENTATION@">