view tool_dependencies.xml @ 1:e1370f7d5e2f draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_macs2_2_1_0_20151222 commit b4ee2876523956e0f887a6f81c2b53b19368604d

<?xml version="1.0"?>
<tool_dependency>
    <package name="numpy" version="1.7.1">
       <repository changeset_revision="300877695495" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="scipy" version="0.12.0">
       <repository changeset_revision="cfbbe183f8a7" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="macs2" version="2.1.0.20151222">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://pypi.python.org/packages/source/M/MACS2/MACS2-2.1.0.20151222.tar.gz</action>

                <action type="set_environment_for_install">
                    <repository changeset_revision="300877695495" name="package_numpy_1_7" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="numpy" version="1.7.1" />
                    </repository>
                    <repository changeset_revision="cfbbe183f8a7" name="package_scipy_0_12" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="scipy" version="0.12.0" />
                    </repository>
                </action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <!-- exporting the CFLAGS and CPPFLAGS are due to http://stackoverflow.com/questions/22313407/clang-error-unknown-argument-mno-fused-madd-python-package-installation-fa -->
                <!-- Addressing compiler compatibility issues for gcc < 4.6 https://github.com/taoliu/MACS/issues/75 --> 
                <action type="shell_command">
                    echo | cc -E - -Ofast; if [ $? -ne 0 ]; then sed -i.bak s/-Ofast/-O3/ setup.py; fi
                </action>
                <action type="shell_command">
                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR/lib/python &amp;&amp;
                    python setup.py install --install-lib $INSTALL_DIR/lib/python --install-scripts $INSTALL_DIR/bin
                </action>
                <action type="set_environment">
                    <environment_variable action="append_to" name="PYTHONPATH">$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="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="append_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable>
                    <environment_variable action="set_to" name="PYTHONPATH_MACS2">$INSTALL_DIR/lib/python</environment_variable>
                    </action>
            </actions>
        </install>
        <readme>Macs2 installation instructions. MACS2 can be found at https://github.com/taoliu/MACS</readme>
    </package>
</tool_dependency>