view tool_dependencies.xml @ 7:54d5b8add0a8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_numpy_1_9 commit 90f0980ded867989e4e3696170d3a2a373aa3197

<?xml version="1.0"?>
<tool_dependency>
        <package name="atlas" version="3.10.2">
            <repository changeset_revision="d5b1c7875b7b" name="package_atlas_3_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
        </package>
        <package name="numpy" version="1.9">
            <install version="1.0">
                <actions>
                    <action type="download_by_url">https://pypi.python.org/packages/source/n/numpy/numpy-1.9.0.tar.gz#md5=510cee1c6a131e0a9eb759aa2cc62609</action>
                    <action type="make_directory">$INSTALL_DIR/lib/python</action>
                    <action type="set_environment_for_install">
                        <repository changeset_revision="d5b1c7875b7b" name="package_atlas_3_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                            <package name="atlas" version="3.10.2" />
                        </repository>
                    </action>
                    <action type="shell_command">
                        export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp; 
                        export ATLAS=$ATLAS_ROOT_PATH &amp;&amp;
                        python 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">$INSTALL_DIR/bin</environment_variable>
                        <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[ATLAS_LIB_DIR]</environment_variable>
                        <environment_variable action="set_to" name="PYTHONPATH_NUMPY">$INSTALL_DIR/lib/python</environment_variable>
                        <environment_variable action="set_to" name="PATH_NUMPY">$INSTALL_DIR/bin</environment_variable>
                    </action>
                </actions>
            </install>
            <readme>Compiling numpy requires a C and Fortran compiler (typically gcc and gfortran). The PYTHONPATH for numpy can be accessed through PYTHONPATH_NUMPY and the binaries with PATH_NUMPY.</readme>
        </package>
</tool_dependency>