<?xml version="1.0"?>
<tool_dependency>
    <!-- UCSC Tools in  -->
    <!-- Useful for HAC are:
        - twoBitInfo
        - sort
        - bedToBigBed
        - gff3ToGenePred
        - gtfToGenePred
        - genePredToBed
        - genePredToBigGenePred
        - faToTwoBit
        - samtools
        - pslToBigPsl
    -->
    <package name="ucsc_tools" version="312">
        <repository changeset_revision="2d6bafd63401" name="package_ucsc_tools_312" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>

    <package name="samtools" version="1.2">
        <repository changeset_revision="f6ae3ba3f3c1" name="package_samtools_1_2" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>

    <!-- TODO: Tools to install -->
    <!-- twoBitInfo / bedToBigBed / faToTwoBit -->


    <!-- Package gff3ToGenePred -->
    <package name="gff3ToGenePred" version="0.0.1">
        <install version="1.0">
            <actions>
                <action target_directory="bin" type="download_binary">
                    <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gff3ToGenePred</url_template>
                    <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gff3ToGenePred</url_template>
                </action>
                <action type="chmod">
                    <file mode="750">$INSTALL_DIR/bin/gff3ToGenePred</file>
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
    </package>

    <!-- Package gtfToGenePred -->
    <package name="gtfToGenePred" version="0.0.1">
        <install version="1.0">
            <actions>
                <action target_directory="bin" type="download_binary">
                    <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/gtfToGenePred</url_template>
                    <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/gtfToGenePred</url_template>
                </action>
                <action type="chmod">
                    <file mode="750">$INSTALL_DIR/bin/gtfToGenePred</file>
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
    </package>

    <!-- Package genePredToBed -->
    <package name="genePredToBed" version="0.0.1">
        <install version="1.0">
            <actions>
                <action target_directory="bin" type="download_binary">
                    <url_template os="darwin">http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/genePredToBed</url_template>
                    <url_template os="linux">http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/genePredToBed</url_template>
                </action>
                <action type="chmod">
                    <file mode="750">$INSTALL_DIR/bin/genePredToBed</file>
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
    </package>

    http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/genePredToBigGenePred

    <!-- Package genePredToBigGenePred -->
    <package name="genePredToBigGenePred" version="0.0.1">
        <install version="1.0">
            <actions>
                <action target_directory="bin" type="download_binary">
                    <url_template os="darwin">
                        http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/genePredToBigGenePred
                    </url_template>
                    <url_template os="linux">
                        http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/genePredToBigGenePred
                    </url_template>
                </action>
                <action type="chmod">
                    <file mode="750">$INSTALL_DIR/bin/genePredToBigGenePred</file>
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
    </package>

    <!-- Package pslToBigPsl -->
    <package name="pslToBigPsl" version="0.0.1">
        <install version="1.0">
            <actions>
                <action target_directory="bin" type="download_binary">
                    <url_template os="darwin">
                        http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.${architecture}/pslToBigPsl
                    </url_template>
                    <url_template os="linux">
                        http://hgdownload.cse.ucsc.edu/admin/exe/linux.${architecture}/pslToBigPsl
                    </url_template>
                </action>
                <action type="chmod">
                    <file mode="750">$INSTALL_DIR/bin/pslToBigPsl</file>
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>The tools downloaded by this dependency definition are free for academic use.</readme>
    </package>
</tool_dependency>