# HG changeset patch
# User sanbi-uwc
# Date 1461052149 14400
# Node ID 3ea25d636c8fa328b07d329ffaeb8f6dd57f4702
# Parent  1f10d92afc681d206ea60eccb4992ec02da4cafb
planemo upload for repository https://github.com/zipho/package_gatk_sanbi_uwc_3_5 commit 71914d46f003625b1badf00fc125a9d2b3fde808

diff -r 1f10d92afc68 -r 3ea25d636c8f tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Apr 19 03:36:54 2016 -0400
+++ b/tool_dependencies.xml	Tue Apr 19 03:49:09 2016 -0400
@@ -2,31 +2,29 @@
 <tool_dependency>
     <package name="gatk_sanbi_uwc" version="3.5">
         <install version="1.0">
-            <actions_group>
-                <actions>
-                    <action type="download_by_url">http://intranet.sanbi.ac.za/GenomeAnalysisTK-3.5.tar.gz</action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                </actions>
+            <actions>
+                <action type="download_by_url">http://intranet.sanbi.ac.za/GenomeAnalysisTK-3.5.tar.gz</action>
+                <action type="move_directory_files">
+                    <source_directory>.</source_directory>
+                    <destination_directory>$INSTALL_DIR/jars</destination_directory>
+                </action>
                 <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="PATH" action="set_to">$INSTALL_DIR/jars</environment_variable>
                 </action>
-            </actions_group>
+            </actions>
         </install>
         <readme>
              <![CDATA[
-                    This package is downloadable only within sanbi uwc network.
+                This package is downloadable only within sanbi uwc network.
 
-                    The Genome Analysis Toolkit or GATK is a software package for analysis of high-throughput sequencing data,
-                    developed by the Data Science and Data Engineering group at the Broad Institute.
+                The Genome Analysis Toolkit or GATK is a software package for analysis of high-throughput sequencing data,
+                developed by the Data Science and Data Engineering group at the Broad Institute.
 
-                    The toolkit offers a wide variety of tools, with a primary focus on variant discovery and
-                    genotyping as well as strong emphasis on data quality assurance.
-                    Its robust architecture, powerful processing engine and high-performance computing features make it
-                    capable of taking on projects of any size.
-            ]]>
+                The toolkit offers a wide variety of tools, with a primary focus on variant discovery and
+                genotyping as well as strong emphasis on data quality assurance.
+                Its robust architecture, powerful processing engine and high-performance computing features make it
+                capable of taking on projects of any size.
+             ]]>
         </readme>
     </package>
 </tool_dependency>
\ No newline at end of file