diff tool_dependencies.xml @ 27:ea9af411907c draft

planemo upload for repository https://github.com/Yating-L/jbrowse-archive-creator.git commit 691e5366893905d30943a3cb8cdfb6341f0f5362-dirty

--- a/tool_dependencies.xml	Fri Oct 13 14:48:17 2017 -0400
+++ b/tool_dependencies.xml	Fri Oct 13 14:51:10 2017 -0400
@@ -4,6 +4,10 @@
         <repository changeset_revision="5b7172f9b230" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
 
+    <package name="ucsc_hac" version="340">
+        <repository changeset_revision="c6311d9e2443" name="package_ucsc_hac_340" owner="yating-l" toolshed="https://testtoolshed.g2.bx.psu.edu" />
+    </package>
+
     <package name="numpy" version="1.9">
         <repository changeset_revision="1e2b7e63dec2" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
     </package>
@@ -47,24 +51,7 @@
             </actions>
         </install>
     </package>
-    
-     <package name="ucsc_tools_340" version="1.0">
-        <install version="1.0">
-            <actions_group>
-                <actions architecture="x86_64" os="linux">
-                    <action type="download_by_url">http://old-gep.wustl.edu/~galaxy/ucsc_tools_340.tar.gz</action>
-                    <action type="move_directory_files">
-                        <source_directory>.</source_directory>                       
-                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
-                    </action>    
-                </actions>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions_group>
-         </install>
-         <readme>The well known UCSC tools from Jim Kent.</readme>
-    </package>
+
     <package name="jbrowse_tools" version="1.12.1">
         <install version="1.0">
             <actions_group>
@@ -93,5 +80,16 @@
          <readme>The perl scripts for converting flat files to json.</readme>
     </package>
 
+    <package name="apollo_api" version="3.0.3">
+        <install version="1.0">
+            <actions>
+                <action type="setup_virtualenv">
+                    apollo==3.0.3
+                </action>
+            </actions>
+        </install>
+    </package>
+
+
     
 </tool_dependency>