<?xml version="1.0"?>
<tool_dependency>
    <package name="openms" version="2.0">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="linux">
                    <action type="download_by_url">https://depot.galaxyproject.org/package/linux/x86_64/openms/openms-2.0-Linux-x86_64.tar.gz</action>
                    <action type="shell_command">rm openms-2.0-Linux-x86_64.tar.gz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                    <action type="set_environment">
                        <environment_variable action="set_to" name="OPENMS_ROOT_PATH">$INSTALL_DIR</environment_variable>
                        <environment_variable action="set_to" name="OPENMS_DATA_PATH">$INSTALL_DIR/share/OpenMS</environment_variable>
                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                        <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
                    </action>
                </actions>
                <actions architecture="x86_64" os="darwin">
                    <action type="download_by_url">https://github.com/OpenMS/OpenMS/archive/develop.tar.gz</action>
                    <action type="download_by_url">https://github.com/OpenMS/contrib/archive/master.tar.gz</action>
                    <action type="shell_command">mv contrib-master ../contrib</action>
                    <package name="libtool" version="2.4">
                        <repository changeset_revision="5ccfb33b5622" name="package_libtool_2_4" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                    </package>
                    <package name="Qt" version="4.8">
                        <repository changeset_revision="d05194d4dc93" name="package_qt_4_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                    </package>
                    <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="bzlib" version="1.0.6">
                        <repository changeset_revision="29f79feefc77" name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
                    </package>
                    <action type="set_environment_for_install">
                        <repository changeset_revision="5ccfb33b5622" name="package_libtool_2_4" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                            <package name="libtool" version="2.4" />
                        </repository>
                        <repository changeset_revision="d05194d4dc93" name="package_qt_4_8" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                            <package name="Qt" version="4.8" />
                        </repository>
                        <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="29f79feefc77" name="package_bzlib_1_0" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
                            <package name="bzlib" version="1.0.6" />
                        </repository>
                    </action>
                    <action type="change_directory">../contrib</action>
                    <action type="shell_command">cmake . -DBUILD_TYPE=SEQAN</action>
                    <action type="shell_command">cmake . -DBUILD_TYPE=LIBSVM</action>
                    <action type="shell_command">cmake . -DBUILD_TYPE=XERCESC</action>
                    <action type="shell_command">cmake . -DBUILD_TYPE=GSL</action>
                    <action type="shell_command">cmake . -DBUILD_TYPE=BOOST -DNUMBER_OF_JOBS=4</action>
                    <action type="shell_command">cmake . -DBUILD_TYPE=COINOR</action>
                    <action type="shell_command">cmake . -DBUILD_TYPE=BZIP2</action>
                    <action type="shell_command">cmake . -DBUILD_TYPE=GLPK</action>
                    <action type="shell_command">cmake . -DBUILD_TYPE=EIGEN</action>
                    <action type="shell_command">cmake . -DBUILD_TYPE=WILDMAGIC</action>

                    <action type="change_directory">..</action>
                    <action type="shell_command">cmake . -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DHAS_XSERVER=OFF -DENABLE_TUTORIALS=OFF -DENABLE_STYLE_TESTING=OFF -DENABLE_UNITYBUILD=OFF -DWITH_GUI=OFF</action>
                    <action type="make_install">OpenMS TOPP UTILS</action>
                    <action type="set_environment">
                        <environment_variable action="set_to" name="OPENMS_ROOT_PATH">$INSTALL_DIR</environment_variable>
                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                        <environment_variable action="set_to" name="OPENMS_DATA_PATH">$INSTALL_DIR/share/OpenMS</environment_variable>
                        <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$INSTALL_DIR/lib</environment_variable>
                        <environment_variable action="prepend_to" name="LD_LIBRARY_PATH">$ENV[QT_ROOT_DIR]/lib/</environment_variable>
                    </action>
                </actions>
            </actions_group>
        </install>
        <readme>
            This package downloads and installs OpenMS.
            http://open-ms.sourceforge.net/
        </readme>
    </package>
</tool_dependency>