# HG changeset patch
# User yating-l
# Date 1490210239 14400
# Node ID 66db979c21f078ff56acea42b331906727ec2735
# Parent  15b4a74722d1b356e3a2573203ea4a0da177a614
planemo upload for repository https://github.com/Yating-L/jbrowse_hub commit 73ede51a133dc8914812195a1b4cd512bfb8f23d-dirty

diff -r 15b4a74722d1 -r 66db979c21f0 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Mar 22 12:07:32 2017 -0400
+++ b/tool_dependencies.xml	Wed Mar 22 15:17:19 2017 -0400
@@ -63,22 +63,25 @@
          <readme>The well known UCSC tools from Jim Kent.</readme>
     </package>
     <package name="jbrowse_tools" version="1.12.1">
-        <install version="1.0">
+        <install version="1.1">
             <actions_group>
                 <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/jbrowse_tools.tar.gz</action>
+                    <action type="download_by_url">http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=105</action>
                     <action type="make_directory">$INSTALL_DIR/jbrowse</action>
+                    <action type="shell_command">
+                        ./setup.sh
+                    </action>
                     <action type="move_directory_files">
                         <source_directory>.</source_directory>                       
                         <destination_directory>$INSTALL_DIR/jbrowse</destination_directory>
                     </action>    
+                    <action type="set_environment">
+                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse</environment_variable>
+                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/bin</environment_variable>
+                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/src</environment_variable>
+                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/extlib</environment_variable>
+                    </action>
                 </actions>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/bin</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/src</environment_variable>
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/jbrowse/extlib</environment_variable>
-                </action>
             </actions_group>
          </install>
          <readme>The perl scripts for converting flat files to json.</readme>