<?xml version="1.0"?>
<tool_dependency>
    <package name="zlib" version="1.2.8">
        <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="grabix" version="0.1.3">
        <repository changeset_revision="8a1184d30e64" name="package_grabix_0_1_3" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="tabix" version="0.2.6">
        <repository changeset_revision="c1743e071a28" name="package_tabix_0_2_6" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="samtools" version="0.1.19">
        <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="bedtools" version="2.19.1">
        <repository changeset_revision="3ad963111153" name="package_bedtools_2_19" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="gemini" version="0.9.1">
        <install version="1.0">
            <actions>
                <!-- first action is always downloading -->
                <action type="download_file">https://raw.github.com/bgruening/gemini-versioned-install/master/gemini_install_0.9.1.py</action>

                <!-- populate the environment variables from the dependend repos -->
                <action type="set_environment_for_install">
                    <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="zlib" version="1.2.8" />
                    </repository>
                    <repository changeset_revision="3ad963111153" name="package_bedtools_2_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                        <package name="bedtools" version="2.19.1" />
                    </repository>
                </action>

                <action type="shell_command">
                    python gemini_install_0.9.1.py $INSTALL_DIR $INSTALL_DIR --nosudo --nodata --notools
                </action>

                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/anaconda/bin</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/gemini/bin</environment_variable>
                    <environment_variable action="set_to" name="GEMINI_ROOT_DIR">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>Compiling GEMINI requires a recent c++ compiler, usually gcc.</readme>
    </package>
</tool_dependency>