view tool_dependencies.xml @ 16:6952a20fa81a draft default tip

planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/segmentation_fold_galaxy_wrapper commit 6545dbf0edf3a0f9afda8d5a27a646253c8f7115

<?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="htseq" version="0.6.1">
        <repository changeset_revision="25da74c1ff6d" name="package_htseq_0_6" owner="iuc" 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="f7d2307f5234c133ad9807c6e5e68312866888ffa993e96ccdbb0f9b7ab5ff62" type="download_by_url">https://github.com/yhoogstrate/segmentation-fold/archive/0ce5f9901e7dcb5d78d750b4df63ab6e03165edb.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>
                    
                    <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="shell_command">
                    cmake -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR .  &amp;&amp;
                    make                                                                    &amp;&amp;
                    make check                                                              &amp;&amp;
                    make install
                </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)
             - c++11 compliant compiler: g++ or clang
        </readme>
    </package>
    
    <package name="segmentation-fold-utils" version="2.0.0">
        <install version="1.0">
            <actions>
                <action sha256sum="f7d2307f5234c133ad9807c6e5e68312866888ffa993e96ccdbb0f9b7ab5ff62" type="download_by_url">https://github.com/yhoogstrate/segmentation-fold/archive/0ce5f9901e7dcb5d78d750b4df63ab6e03165edb.tar.gz</action>
                
                <!-- Also install the python utils -->
                <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>

                     <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>

                    <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>

                    <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>
                    
                    <repository changeset_revision="25da74c1ff6d" name="package_htseq_0_6" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="htseq" version="0.6.1" />
                    </repository>
                    
                    <package sha256sum="cc6a19da8ebff6e7074f731447ef7e112bd23adf3de5c597cf9989f2fd8defe9">https://pypi.python.org/packages/7a/00/c14926d8232b36b08218067bcd5853caefb4737cda3f0a47437151344792/click-6.6.tar.gz</package>
                </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:$INSTALL_DIR/lib64/python"  &amp;&amp;
                    cd scripts/energy-estimation-utility                                               &amp;&amp;
                    echo "---------------------------------------------------------------------------" &amp;&amp;
                    head -n 161 segmentation_fold_utils/XMLFile.py | tail -n 11                        &amp;&amp;
                    echo "---------------------------------------------------------------------------" &amp;&amp;
                    python setup.py install --home "$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>
                </action>
            </actions>
        </install>
        <readme>
            Installation of segmentation-fold-utils requires:
             - Python                       (via toolshed)
             - numpy                        (via toolshed)
             - pysam                        (via toolshed)
        </readme>
    </package>
</tool_dependency>