annotate tool_dependencies.xml @ 62:b90441d0fe7d

Undo including $ENV[PYTHONPATH] in PYTHONPATH If $ENV[PYTHONPATH] is empty, Galaxy replaces it with $PYTHONPATH instead of an empty string, which introduces python 2 code in the python 3 path.

<?xml version="1.0"?>
<tool_dependency>
  <package name="libxml2" version="2.9.1">
    <repository name="package_libxml2_2_9_1" owner="devteam" prior_installation_required="True"
                toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="3af7ad13a6fb" />
  </package>

  <package name="libxslt" version="1.1.28">
    <repository name="package_libxslt_1_1_28" owner="devteam" prior_installation_required="True"
                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="7719329e5b98" />
  </package>
  
  <package name="blast2html_venv" version="0.1">
    <install version="1.0">
      <actions>
        <action type="set_environment_for_install">
          <repository name="package_libxml2_2_9_1" owner="devteam"
                      toolshed="http://toolshed.g2.bx.psu.edu" changeset_revision="3af7ad13a6fb">
            <package name="libxml2" version="2.9.1" />
          </repository>
          <repository name="package_libxslt_1_1_28" owner="devteam"
                      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="7719329e5b98">
            <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="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>
        </action>
      </actions>
    </install>
    <readme>A Python 3 virtual environment that includes the python packages blast2html depends on, which are lxml and jinja2.</readme>
  </package>

</tool_dependency>