Mercurial > repos > iuc > package_openms_2_0
changeset 0:4c9d21e76786 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_openms_2_0 commit 0c094c3df9574cb057ccb65878f98f300d5b0a09
| author | iuc |
|---|---|
| date | Tue, 19 May 2015 14:59:55 -0400 |
| parents | |
| children | |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 83 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue May 19 14:59:55 2015 -0400 @@ -0,0 +1,83 @@ +<?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>