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<?xml version="1.0"?>
<tool_dependency>
    <!--
        pysam has had several internal changes in 0.7.*, 0.8.1, 0.8.2 &
        0.8.3 and therefore FlaiMapper is not compatible with all of
        them. For compatibility this package is provided with pysam
        0.8.2.1 which was not originally in the toolshed.
    -->
    <package name="pysam" version="0.8.2.1">
        <repository changeset_revision="f8fecf1f6eba" name="package_pysam_0_8_2" owner="yhoogstrate" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    
    <package name="flaimapper" version="1.2.1">
        <install version="1.0">
            <actions>
                <action type="set_environment_for_install">
                    <repository changeset_revision="f8fecf1f6eba" name="package_pysam_0_8_2" owner="yhoogstrate" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="pysam" version="0.8.2.1" />
                    </repository>
                </action>
                
                <action type="make_directory">$INSTALL_DIR/bin</action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="make_directory">$INSTALL_DIR/lib64/python</action>
                
                <action type="shell_command">
                    git clone https://github.com/yhoogstrate/flaimapper flaimapper &amp;&amp;
                    cd flaimapper                                                  &amp;&amp;
                    git reset --hard d3cc32a10ba3d33fde4cb76e8013a51ec8bdf779      &amp;&amp;
                    
                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR                     &amp;&amp;
                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR"/lib/python"        &amp;&amp;
                    export PYTHONPATH=$PYTHONPATH:$INSTALL_DIR"/lib64/python"      &amp;&amp;
                    export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH                      &amp;&amp;
                    export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH"/lib/python"         &amp;&amp;
                    export PYTHONPATH=$PYTHONPATH:$PYSAM_PATH"/lib64/python"       &amp;&amp;
                    
                    cd src                                                         &amp;&amp;
                    
                    python setup.py build                                          &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">$INSTALL_DIR:$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>
            Downloads and installs FlaiMapper.
            
            Prerequisites:
                - Python
                - git
            
            Because I accidentally included too much large files within
            the GitHub repository of FlaiMapper, it has become large.
            This is the reason why installation takes a while.
        </readme>
    </package>
</tool_dependency>