# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1347627083 18000
# Node ID ceaa79a5ee166a193e01fab50c382e6d4a8cd1ff
# Parent  458d28b65750c04f786ea233f3b69c3bf77cf226
Actions for tool_dependencies.xml

diff -r 458d28b65750 -r ceaa79a5ee16 tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Sep 14 07:26:01 2012 -0500
+++ b/tool_dependencies.xml	Fri Sep 14 07:51:23 2012 -0500
@@ -1,16 +1,33 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <set_environment version="1.0">
-        <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/dist</environment_variable>
+        <environment_variable name="JAVA_JAR_PATH" action="set_to">$INSTALL_DIR/bin</environment_variable>
     </set_environment>
     <package name="snpEff" version="3.0f">
         <install version="1.0">
             <actions>
                 <action type="download_by_url">http://sourceforge.net/projects/snpeff/files/snpEff_latest_core.zip/download</action>
-                <action type="shell_command">mkdir -p $INSTALL_DIR/dist/</action>
                 <action type="shell_command">pwd</action>
                 <action type="shell_command">ls</action>
-                <action type="shell_command">cp -rp *  $INSTALL_DIR/dist/</action>
+                <action type="move_file">
+                    <source>SnpSift.jar</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_file">
+                    <source>snpEff.jar</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>scripts</source_directory>
+                    <destination_directory>$INSTALL_DIR/bin</destination_directory>
+                </action>
+                <action type="move_file">
+                    <source>snpEff.config</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable
+                </action>
             </actions>
         </install>
         <readme>