<?xml version="1.0"?>
<tool_dependency>
    <package name="deepTools" version="1.5.9">
        <install version="1.0">
            <actions>
                <action type="download_by_url">https://github.com/fidelram/deepTools/archive/1.5.9.1.tar.gz</action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="64e2daea7b15" name="package_pysam_0_7_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="pysam" version="0.7.7" />
                    </repository>
                    <repository changeset_revision="4c15bd2528e1" name="package_bx_python_0_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="bx-python" version="0.7.1" />
                    </repository>
                    <repository changeset_revision="6a7842f2f960" name="package_numpy_1_7" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="numpy" version="1.7.1" />
                    </repository>
                    <repository changeset_revision="b08a9f0f28ec" name="package_matplotlib_1_2" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="matplotlib" version="1.2.1" />
                    </repository>
                    <repository changeset_revision="6d8201c2a767" name="package_scipy_0_12" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="scipy" version="0.12.0" />
                    </repository>
                    <repository changeset_revision="0e56e4dac6e7" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="samtools" version="0.1.19" />
                    </repository>
                    <repository changeset_revision="535261946ba0" name="package_ucsc_tools" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="ucsc_tools" version="0.1" />
                    </repository>
                </action>
                <action type="make_directory">$INSTALL_DIR/lib/python</action>
                <action type="shell_command">
                    export PYTHONPATH=$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="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable action="prepend_to" name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable action="set_to" name="DEEPTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
                    <environment_variable action="set_to" name="DEEPTOOLS_PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
                    <environment_variable action="set_to" name="DEEPTOOLS_PATH">$INSTALL_DIR/bin</environment_variable>
                    <!-- include samtools into PATH -->
                    <environment_variable action="prepend_to" name="PATH">$ENV[BAM_ROOT]/bin</environment_variable>
                    <!-- include numpy -->
                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_NUMPY]</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_NUMPY]</environment_variable>
                    <!-- include matplotlib -->
                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_MATPLOTLIB]</environment_variable>
                    <!-- include scipy -->
                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYTHONPATH_SCIPY]</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$ENV[PATH_SCIPY]</environment_variable>
                    <!-- include bx-python -->
                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[BX_PYTHON_PATH]/lib/python</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$ENV[BX_PYTHON_PATH]/bin</environment_variable>
                    <!-- include pysam -->
                    <environment_variable action="prepend_to" name="PYTHONPATH">$ENV[PYSAM_PATH]/lib/python</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$ENV[PYSAM_PATH]/bin</environment_variable>
                    <!-- include ucsc tools -->
                    <environment_variable action="prepend_to" name="PATH">$ENV[UCSC_TOOLS_ROOT_PATH]</environment_variable>

                    <!-- disable the config file of deepTools -->
                    <environment_variable action="set_to" name="DEEP_TOOLS_NO_CONFIG">TRUE</environment_variable>
                </action>
             </actions>
         </install>
         <readme>
            Installation of deepTools from Fidel Ramirez.
            https://github.com/fidelram/deepTools
         </readme>
     </package>
</tool_dependency>