diff tool_dependencies.xml @ 0:028babd7a6c5 draft default tip

Try at a fresh start...

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Mar 29 17:30:07 2013 -0400
@@ -0,0 +1,37 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="ontologizer-jar" version="0.0.3">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url" target_filename="ontologizer.jar">http://compbio.charite.de/contao/index.php/cmdlineOntologizer.html?file=tl_files/ontologizer/cmdline/Ontologizer.jar</action>
+                <action type="move_file">
+                    <source>ontologizer.jar</source>
+                    <destination>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="ONTOLOGIZER_JAR" action="set_to">$INSTALL_DIR/bin/ontologizer.jar</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+            ontologizer requires java and curl to be installed.
+        </readme>
+    </package>
+    <package name="obo-scripts" version="1.0.12">
+        <install version="1.0">
+            <actions>
+                <action type="shell_command">git clone http://github.com/cmungall/obo-scripts</action>
+                <action type="move_directory_files">
+                    <source_directory>./</source_directory>
+                    <destination_directory>$INSTALL_DIR</destination_directory>
+                </action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+          obo_scripts require perl to be installed.
+      </readme>
+  </package>
+</tool_dependency>