annotate tool_dependencies.xml @ 0:25b635f2eaa5 draft

Imported from capsule None

<?xml version="1.0"?>
<tool_dependency>
  <package name="numpy" version="1.9">
      <repository changeset_revision="03eea94e534e" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="scipy" version="0.14">
      <repository changeset_revision="36b2ca3477c2" name="package_scipy_0_14" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="matplotlib" version="1.2.1">
      <repository changeset_revision="fe60617380df" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="scikit_learn" version="0.15">
      <install version="1.0">
          <actions>
              <action type="download_by_url">https://pypi.python.org/packages/source/s/scikit-learn/scikit-learn-0.15.2.tar.gz#md5=d9822ad0238e17b382a3c756ea94fe0d</action>
                <action type="set_environment_for_install">
                  <repository changeset_revision="03eea94e534e" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                      <package name="numpy" version="1.9" />
                    </repository>
                    <repository changeset_revision="36b2ca3477c2" name="package_scipy_0_14" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                      <package name="scipy" version="0.14" />
                    </repository>
                    <repository changeset_revision="fe60617380df" name="package_matplotlib_1_2" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                      <package name="matplotlib" version="1.2.1" />
                    </repository>
                </action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action language="cheetah" type="template_command">
                    export PYTHONPATH=\$PYTHONPATH:$env.INSTALL_DIR/lib/python &amp;&amp; 

                    export PATH=\$PATH:$env.PATH_NUMPY &amp;&amp; 
                    export PYTHONPATH=\$PYTHONPATH:$env.PYTHONPATH_NUMPY:$env.PYTHONPATH_SCIPY:$env.PYTHONPATH_MATPLOTLIB &amp;&amp;

                    python setup.py install --install-lib $env.INSTALL_DIR/lib/python
                    </action>
                <action type="set_environment">
                  <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_SCIPY]</environment_variable>
                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable>
                    <environment_variable action="set_to" name="PYTHONPATH_SCIKIT_LEARN">$INSTALL_DIR/lib/python</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            Compiling scikit-learn requires a C compiler (typically gcc). 
            The PYTHONPATH for scikit-learn can be accessed through PYTHONPATH_SCIKIT_LEARN.
            
            Wrapper development: https://github.com/bgruening/galaxytools/tree/master/orphan_tool_dependencies
            </readme>
    </package>
</tool_dependency>