annotate tool_dependencies.xml @ 0:8433ee4531ff draft

planemo upload for repository https://github.com/biopython/galaxy_packages/tree/master/package_biopython_1_66 commit 985e29ac10e02dd97a3e155d881513658448e85a

<?xml version="1.0"?>
<tool_dependency>
    <package name="numpy" version="1.9">
        <repository changeset_revision="9cc1138e5e3e" name="package_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="biopython" version="1.66">
        <readme>
This Galaxy Tool Shed package installs Biopython from source, having
first installed NumPy which is a build time depencency. This requires
and assumes a standard C compiler is already installed, along with
the Python header files.

Development of this dependency definition is being done here on GitHub:
https://github.com/biopython/galaxy_packages

The PYTHONPATH for biopython can be accessed through PYTHONPATH_BIOPYTHON.
        </readme>
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://pypi.python.org/packages/source/b/biopython/biopython-1.66.tar.gz</action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="9cc1138e5e3e" name="package_numpy_1_9" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="numpy" version="1.9" />
                    </repository>
                </action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="shell_command">
                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
                    export PATH=$PATH:$PATH_NUMPY &amp;&amp; 
                    export PYTHONPATH=$PYTHONPATH:$PYTHONPATH_NUMPY &amp;&amp; 
                    python setup.py install --install-lib $INSTALL_DIR/lib/python
                </action>
                <action type="set_environment">
                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
                    <environment_variable action="set_to" name="PYTHONPATH_BIOPYTHON">$INSTALL_DIR/lib/python</environment_variable>
                </action>
            </actions>
        </install>
    </package>
</tool_dependency>