diff tool_dependencies.xml @ 53:4217bb9cf1d3

depend on python 3; fix internal links with multiple iterations

--- a/tool_dependencies.xml	Wed May 21 18:39:51 2014 +0200
+++ b/tool_dependencies.xml	Mon May 26 13:07:13 2014 +0200
@@ -15,29 +15,12 @@
                 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee" />
   </package>
 
-  <package name="argparse" version="1.2.1">
-    <install version="1.0">
-      <actions>
-        <action type="setup_virtualenv">
-          argparse == 1.2.1
-        </action>
-      </actions>
-    </install>
-    <readme>The Python argparse library. This is included in the stdlib for python 2.7 and up, but not for 2.6</readme>
+  <package name="python3" version="3.4.1">
+    <repository name="package_python3_4" owner="jankanis" prior_installation_required="True"
+                toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="9dbfc4fcef0a" />
   </package>
-
-  <package name="python_six" version="1.3.0">
-    <install version="1.0">
-      <actions>
-        <action type="setup_virtualenv">
-          six >= 1.3.0
-        </action>
-      </actions>
-    </install>
-    <readme>The Python six library for python 2/3 compatibility</readme>
-  </package>
-
-  <package name="lxml" version="2.2.3">
+  
+  <package name="blast2html_venv" version="0.1">
     <install version="1.0">
       <actions>
         <action type="set_environment_for_install">
@@ -53,29 +36,27 @@
                       toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee">
             <package name="libxslt" version="1.1.28" />
           </repository>
+          <repository name="python3" owner="jankanis">
+            <package name="python3" version="3.4.1" />
+          </repository>
         </action>
-	<action type="shell_command">
-	  echo '*******************************************************************************'
-	  echo $PATH
-	  echo xslt-config at: `which -a xslt-config`
-	</action>
-        <action type="setup_virtualenv">
-          lxml == 2.2.3
+        
+        <action type="shell_command">
+          # Unset any saved environment settings from parent virtual
+          # environments, e.g. for python 2 or if Galaxy itself is running
+          # from within a virtual environment.
+          unset _OLD_VIRTUAL_PATH; unset _OLD_VIRTUAL_PYTHONHOME
+          pyvenv blast2html_venv
+          . blast2html_venv/bin/activate
+          pip3 install lxml jinja2
+        </action>
+        
+        <action type="set_environment">
+          <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/python3.4/site-packages</environment_variable>
         </action>
       </actions>
     </install>
-    <readme>The Python lxml library</readme>
-  </package>
-
-  <package name="jinja2" version="2.7.2">
-    <install version="1.0">
-      <actions>
-        <action type="setup_virtualenv">
-          jinja2 == 2.7.2
-        </action>
-      </actions>
-    </install>
-    <readme>The Jinja 2 template engine for Python</readme>
+    <readme>A Python 3 virtual environment that includes the python packages blast2html depends on, which are lxml and jinja2.</readme>
   </package>
 
 </tool_dependency>