Mercurial > repos > jankanis > blast2html

diff tool_dependencies.xml @ 58:39df29f647e8

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set other environment variables as well
author Jan Kanis <jan.code@jankanis.nl>
date Tue, 27 May 2014 12:45:50 +0200
parents 159989f6bfa6
children cd31e2fb5f22
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--- a/tool_dependencies.xml	Mon May 26 15:34:54 2014 +0200
+++ b/tool_dependencies.xml	Tue May 27 12:45:50 2014 +0200
@@ -39,12 +39,15 @@
           # from within a virtual environment.
           unset _OLD_VIRTUAL_PATH; unset _OLD_VIRTUAL_PYTHONHOME
           pyvenv blast2html_venv
-          . blast2html_venv/bin/activate
-          pip3 install lxml jinja2
+          blast2html_venv/bin/pip3 install lxml jinja2
         </action>
         
         <action type="set_environment">
-          <environment_variable name="PYTHONPATH" action="prepend_to">$INSTALL_DIR/lib/python3.4/site-packages</environment_variable>
+	  <!-- Remove any incoming PYTHONPATH elements from Galaxy's own environment -->
+          <environment_variable name="PYTHONPATH" action="set_to">$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>
         </action>
       </actions>