Mercurial > repos > pjbriggs > trimmomatic

diff tool_dependencies.xml @ 5:f80107cdc406 draft

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Updated to 0.36.1: Reimplement to work with bioconda Trimmomatic 0.36 (toolshed version is still supported for now).
author pjbriggs
date Fri, 16 Dec 2016 11:31:55 -0500
parents 14d05f2d511d
children
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--- a/tool_dependencies.xml	Thu Jul 14 09:17:38 2016 -0400
+++ b/tool_dependencies.xml	Fri Dec 16 11:31:55 2016 -0500
@@ -4,7 +4,7 @@
       <install version="1.0">
 	<actions>
 	  <action type="download_by_url">http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic/Trimmomatic-0.36.zip</action>
-	  <action type="move_file">
+	  <action type="move_file" rename_to="trimmomatic.jar">
 	    <source>trimmomatic-0.36.jar</source>
 	    <destination>$INSTALL_DIR</destination>
 	  </action>
@@ -13,10 +13,10 @@
             <destination_directory>$INSTALL_DIR/adapters</destination_directory>
           </action>
 	  <action type="set_environment">
-	    <environment_variable name="TRIMMOMATIC_DIR" action="set_to">$INSTALL_DIR</environment_variable>
+	    <environment_variable name="TRIMMOMATIC_JAR_PATH" action="set_to">$INSTALL_DIR</environment_variable>
 	  </action>
 	  <action type="set_environment">
-	    <environment_variable name="TRIMMOMATIC_ADAPTERS_DIR" action="set_to">$INSTALL_DIR/adapters</environment_variable>
+	    <environment_variable name="TRIMMOMATIC_ADAPTERS_PATH" action="set_to">$INSTALL_DIR/adapters</environment_variable>
 	  </action>
 	</actions>
       </install>