comparison tool_dependencies.xml @ 0:a6b5d3d4825c draft

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit d7ca394c8959cf2a0d9c38fa4de309be99c73280-dirty

0:a6b5d3d4825c

<?xml version="1.0"?>
<tool_dependency>
    <package name="boost" version="1.57">
        <repository changeset_revision="a0dd39685fce" name="package_boost_1_57" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    
    <package name="cmake" version="3.2.3">
        <repository changeset_revision="1aea698a1c63" name="package_cmake_3_2_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    
    <package name="python" version="2.7.10">
        <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    
    <package name="segmentation-fold" version="1.6.2">
        <install version="1.0">
            <actions>
                <action sha256sum="6c7c1e21413a9841fd4822e1ff85e3b44a7684117617e1388c515475f7c1869b" type="download_by_url">https://github.com/yhoogstrate/segmentation-fold/archive/v1.6.3.tar.gz</action>
                    
                <action type="set_environment_for_install">
                    <repository changeset_revision="a0dd39685fce" name="package_boost_1_57" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="boost" version="1.57" />
                    </repository>
                </action>
                
                <action type="set_environment_for_install">
                    <repository changeset_revision="1aea698a1c63" name="package_cmake_3_2_3" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="cmake" version="3.2.3" />
                    </repository>
                </action>
                
                <action type="shell_command">
                    cmake -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR .  &amp;&amp;
                    make                                                                    &amp;&amp;
                    make check                                                              &amp;&amp;
                    make install
                </action>
                
                <!-- Also install the python utils -->
                <action type="set_environment_for_install">
                     <repository changeset_revision="0339c4a9b87b" name="package_python_2_7_10" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="python" version="2.7.10" />
                    </repository>
                </action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="make_directory">$INSTALL_DIR/lib64/python</action>
                <action type="shell_command">
                    export PYTHONPATH="$PYTHONPATH:$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python"  &amp;&amp;
                    cd scripts/energy-estimation-utility                                               &amp;&amp;
                    python setup.py install --home "$INSTALL_DIR" --install-scripts "$INSTALL_DIR/bin"
                </action>
                
                <action type="set_environment">
                    <environment_variable action="append_to" name="PYTHONPATH">$INSTALL_DIR/lib/python:$INSTALL_DIR/lib64/python</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="set_to" name="SEGMENTATION_FOLD_DEFAULT_XML">$INSTALL_DIR/share/segmentation-fold/segments.xml</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
            Installation of segmentation-fold requires:
             - libboost                     (via toolshed)
             - CMake                        (via toolshed)
             - Python (for energy utils)    (via toolshed)
             - c++11 compliant compiler: g++ or clang
        </readme>
    </package>
</tool_dependency>