Mercurial > repos > yhoogstrate > package_segmentation_fold_1_6_5

view tool_dependencies.xml @ 3:1c7d6b167510 draft

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planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit fb0bbb26638c0185ef16efa2e0ac3952d671b711-dirty
author yhoogstrate
date Thu, 19 May 2016 03:29:32 -0400
parents bf60a5f98e16
children e3ef4c5b6f19
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<?xml version="1.0"?>
<tool_dependency>
    <package name="boost" version="1.57">
        <repository changeset_revision="bd65814f17c5" name="package_boost_1_57" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    
    <package name="cmake" version="3.2.3">
        <repository changeset_revision="2da7b99cb1a1" name="package_cmake_3_2_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    
    <package name="python" version="2.7.10">
        <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="numpy" version="1.9">
        <repository changeset_revision="fe0870696ca7" name="package_python_2_7_numpy_1_9" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="pysam" version="0.8.2.1">
        <repository changeset_revision="e6c1f548397a" name="package_pysam_0_8_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    
    <package name="setuptools" version="19.0">
        <repository changeset_revision="c0a6821af233" name="package_setuptools_19_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    
    <package name="segmentation-fold" version="1.6.5">
        <install version="1.0">
            <actions>
                <action sha256sum="f7dfbc70313aa2502dd35692f33bf06ef32c17594a526ea054cf369837aad794" type="download_by_url">https://github.com/yhoogstrate/segmentation-fold/archive/3cce35ab2265caf186c492764afb5a71ae55d80d.tar.gz</action>
                    
                <action type="set_environment_for_install">
                    <repository changeset_revision="bd65814f17c5" name="package_boost_1_57" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="boost" version="1.57" />
                    </repository>
                </action>
                
                <action type="set_environment_for_install">
                    <repository changeset_revision="2da7b99cb1a1" name="package_cmake_3_2_3" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="cmake" version="3.2.3" />
                    </repository>
                </action>
                
                <action type="set_environment_for_install">
                    <repository changeset_revision="c0a6821af233" name="package_setuptools_19_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="setuptools" version="19.0" />
                    </repository>
                </action>
                
                <action type="shell_command">
                    ls
                </action>
                
                <!-- Also install the python utils -->
                <action type="set_environment_for_install">
                     <repository changeset_revision="a28e3c30828d" name="package_python_2_7_10" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="python" version="2.7.10" />
                    </repository>
                </action>
                
                <action type="set_environment_for_install">
                    <repository changeset_revision="fe0870696ca7" name="package_python_2_7_numpy_1_9" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="numpy" version="1.9" />
                    </repository>
                </action>
                
                <action type="set_environment_for_install">
                    <repository changeset_revision="e6c1f548397a" name="package_pysam_0_8_2" owner="yhoogstrate" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="pysam" version="0.8.2.1" />
                    </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>