annotate tool_dependencies.xml @ 0:4c9d21e76786 draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_openms_2_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09

<?xml version="1.0"?>
<!-- ToDo can we get it easily without svn? Is this included in the final tarball? -->
<!-- svn checkout http://svn.code.sf.net/p/open-ms/code/THIRDPARTY/SEARCHENGINES/Linux/64bit/ _searchengines -->
<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 name="package_libtool_2_4" owner="iuc" prior_installation_required="True" />
                    </package>
                    <package name="Qt" version="4.8">
                        <repository name="package_qt_4_8" owner="iuc" prior_installation_required="True" />
                    </package>
                    <package name="zlib" version="1.2.8">
                        <repository name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" />
                    </package>
                    <package name="bzlib" version="1.0.6">
                        <repository name="package_bzlib_1_0" owner="iuc" prior_installation_required="True" />
                    </package>
                    <action type="set_environment_for_install">
                        <repository name="package_libtool_2_4" owner="iuc">
                            <package name="libtool" version="2.4" />
                        </repository>
                        <repository name="package_qt_4_8" owner="iuc">
                            <package name="Qt" version="4.8" />
                        </repository>
                        <repository name="package_zlib_1_2_8" owner="iuc">
                            <package name="zlib" version="1.2.8" />
                        </repository>
                        <repository name="package_bzlib_1_0" owner="iuc">
                            <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=$INSTALL_DIR -DHAS_XSERVER=OFF -DENABLE_TUTORIALS=OFF -DENABLE_STYLE_TESTING=OFF -DENABLE_UNITYBUILD=OFF -DWITH_GUI=OFF</action>
                    <action type="shell_command">make OpenMS TOPP UTILS</action>
                    <action type="shell_command">make install</action>
                    <action type="set_environment">
                        <environment_variable action="set_to" name="OPENMS_ROOT_PATH">$INSTALL_DIR</environment_variable>
                        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                        <environment_variable action="set_to" name="OPENMS_DATA_PATH">$INSTALL_DIR/share/OpenMS</environment_variable>
                        <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$INSTALL_DIR/lib</environment_variable>
                        <environment_variable name="LD_LIBRARY_PATH" action="prepend_to">$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>