Mercurial > repos > jankanis > blast2html2

changeset 84:4340432b7191 default

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Backed out changesets 0b5819dc1478 and 3338571b44cd to create new release version
author Jan Kanis <jan.code@jankanis.nl>
date Tue, 24 Jun 2014 11:00:57 +0200
parents 0b5819dc1478
children 2edb77030a9e
files blast2html.xml tool_dependencies.xml
diffstat 2 files changed, 24 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/blast2html.xml	Mon Jun 23 17:46:26 2014 +0200
+++ b/blast2html.xml	Tue Jun 24 11:00:57 2014 +0200
@@ -6,7 +6,7 @@
       <requirement name="package" version="0.1">blast2html_venv</requirement>
     </requirements>
     
-    <command interpreter="python2">blast2html.py -i "${input}" -o "${output}"</command>
+    <command interpreter="python3">blast2html.py -i "${input}" -o "${output}"</command>
 
     <stdio>
       <!-- Any exit code other than 0 is an error -->
--- a/tool_dependencies.xml	Mon Jun 23 17:46:26 2014 +0200
+++ b/tool_dependencies.xml	Tue Jun 24 11:00:57 2014 +0200
@@ -10,6 +10,11 @@
                 toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee" />
   </package>
 
+  <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="d30e6a97dfbf" />
+  </package>
+  
   <package name="blast2html_venv" version="0.1">
     <install version="1.0">
       <actions>
@@ -22,14 +27,26 @@
                       toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="039b04adcfee">
             <package name="libxslt" version="1.1.28" />
           </repository>
+          <repository name="package_python3_4" owner="jankanis"
+                      toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="d30e6a97dfbf">
+            <package name="python3" version="3.4.1" />
+          </repository>
         </action>
-
-	<action type="setup_virtualenv">
-	  lxml==3.3.5
-	  jinja2==2.7.3
-	</action>
+        
+        <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/pip3 install lxml jinja2
+        </action>
         
         <action type="set_environment">
+          <!-- Remove any incoming PYTHONPATH elements from Galaxy's own environment -->
+          <environment_variable name="PYTHONPATH" action="set_to">$INSTALL_DIR/blast2html_venv/lib/python3.4/site-packages</environment_variable>
+          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/blast2html_venv/bin</environment_variable>
+          <environment_variable name="PYTHONHOME" action="set_to"></environment_variable>
           <!-- To find shared libraries such as libssl or libxml2 -->
           <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$ENV[LD_LIBRARY_PATH]</environment_variable>
           <!-- libxml2 doesn't actually export its own LD_LIBRARY_PATH -->
@@ -37,7 +54,7 @@
         </action>
       </actions>
     </install>
-    <readme>A Python 2 virtual environment that includes the python packages blast2html depends on, which are lxml and jinja2.</readme>
+    <readme>A Python 3 virtual environment that includes the python packages blast2html depends on, which are lxml and jinja2.</readme>
   </package>
 
 </tool_dependency>