Mercurial > repos > jankanis > blast2html

changeset 84:3338571b44cd draft

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first attempt at running on python 2.6
author Jan Kanis <jan.code@jankanis.nl>
date Mon, 23 Jun 2014 17:11:58 +0200
parents 40ce2043006a
children 0b5819dc1478
files blast2html.xml tool_dependencies.xml
diffstat 2 files changed, 7 insertions(+), 24 deletions(-) [+]
line wrap: on
line diff
--- a/blast2html.xml	Thu Jun 19 17:00:29 2014 +0200
+++ b/blast2html.xml	Mon Jun 23 17:11:58 2014 +0200
@@ -6,7 +6,7 @@
       <requirement name="package" version="0.1">blast2html_venv</requirement>
     </requirements>
     
-    <command interpreter="python3">blast2html.py -i "${input}" -o "${output}"</command>
+    <command interpreter="python2">blast2html.py -i "${input}" -o "${output}"</command>
 
     <stdio>
       <!-- Any exit code other than 0 is an error -->
--- a/tool_dependencies.xml	Thu Jun 19 17:00:29 2014 +0200
+++ b/tool_dependencies.xml	Mon Jun 23 17:11:58 2014 +0200
@@ -10,11 +10,6 @@
                 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>
@@ -27,26 +22,14 @@
                       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="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="setup_virtualenv">
+	  lxml==2.9.1
+	  jinja2==2.7.3
+	</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 -->
@@ -54,7 +37,7 @@
         </action>
       </actions>
     </install>
-    <readme>A Python 3 virtual environment that includes the python packages blast2html depends on, which are lxml and jinja2.</readme>
+    <readme>A Python 2 virtual environment that includes the python packages blast2html depends on, which are lxml and jinja2.</readme>
   </package>
 
 </tool_dependency>