annotate tool_dependencies.xml @ 0:aaeb6262be47 draft default tip

planemo upload for repository https://github.com/phac-nml/galaxy_tools/tree/master/packages/package_python_3_4_scipy_0_16 commit e2554dc878f6abf1c02ed9e6e4f4440ed32b02aa

<?xml version="1.0"?>
<tool_dependency>
    <package name="atlas" version="3.10.2">
        <repository changeset_revision="98c017ec230d" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="python" version="3.4">
        <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="numpy" version="1.10.1">
        <repository changeset_revision="f182da2b1d78" name="package_python_3_4_numpy_1_10_1" owner="nml" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="scipy" version="0.16">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://pypi.python.org/packages/source/s/scipy/scipy-0.16.0.tar.gz</action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="98c017ec230d" name="package_atlas_3_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="atlas" version="3.10.2" />
                    </repository>
                    <repository changeset_revision="20ecf5cd3c0e" name="package_python_3_4" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="python" version="3.4" />
                    </repository>
                    <repository changeset_revision="f182da2b1d78" name="package_python_3_4_numpy_1_10_1" owner="nml" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="numpy" version="1.10.1" />
                    </repository>
                </action>
                <action type="make_directory">$INSTALL_DIR/bin</action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="shell_command">python3 setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin</action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PYTHONPATH">$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">$ENV[PATH_NUMPY]</environment_variable>
                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[ATLAS_LIB_DIR]</environment_variable>
                    <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[ATLAS_LIB_DIR]/atlas</environment_variable>
                    <environment_variable action="set_to" name="PYTHONPATH_SCIPY">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable action="set_to" name="PATH_SCIPY">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="set_to" name="SCIPY_ROOT_DIR">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>Compiling scipy requires a C and Fortran compiler (typically gcc and gfortran). The PYTHONPATH for scipy can be accessed through PYTHONPATH_SCIPY and the binaries with PATH_SCIPY.</readme>
    </package>
</tool_dependency>