annotate tool_dependencies.xml @ 3:47251581daf6 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_gemini_0_10_0 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty

<?xml version="1.0"?>
<tool_dependency>
    <package name="zlib" version="1.2.8">
        <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="grabix" version="0.1.3">
        <repository changeset_revision="0714d88bd854" name="package_grabix_0_1_3" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="tabix" version="0.2.6">
        <repository changeset_revision="3d6beba7393e" name="package_tabix_0_2_6" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="samtools" version="0.1.19">
        <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="bedtools" version="2.19.1">
        <repository changeset_revision="fb3a854c7104" name="package_bedtools_2_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="gemini" version="0.10.0">
        <install version="1.0">
            <actions>
                <!-- first action is always downloading -->
                <action type="download_file">https://raw.github.com/arq5x/gemini/master/gemini/scripts/gemini_install.py</action>

                <!-- populate the environment variables from the dependend repos -->
                <action type="set_environment_for_install">
                    <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="zlib" version="1.2.8" />
                    </repository>
                </action>

                <action type="shell_command">
                    export HOME=$INSTALL_DIR &amp;&amp; python gemini_install.py $INSTALL_DIR $INSTALL_DIR --nosudo --nodata --notools --gemini-version 0.10.0
                </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>
                    <environment_variable action="set_to" name="HOME">.</environment_variable>
                </action>
            </actions>
        </install>
        <readme>Compiling GEMINI requires a recent c++ compiler, usually gcc.</readme>
    </package>
</tool_dependency>