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Building OpenMS on Mac OS X

Read this section first!

This document addresses OpenMS users and explains the installation procedure for building OpenMS from its sources. If you only want to use the OpenMS Proteomics Pipeline (TOPP), you are strongly encouraged to download the binary installer (see here), instead of building OpenMS from sources. Be aware though that we do not provide binary installers for every MacOS version. For more information read the install instructions for the TOPP binaries.

This document especially considers the installation of several libraries which are required by OpenMS. Most of these libraries are made available in our "contrib-package" (see below).
If you encounter errors during configuring/compiling our software, have a look at our "Known Issues" section (documentation), maybe the error is already known. If not, please write to the mailing list.

Required applications

In order to compile OpenMS, several applications need to be installed:

If your OpenMS version is a development version from SVN, the following applications are needed in order to create the OpenMS documentation:


Installing the contrib package

In order to facilitate the installation of the libraries required for OpenMS, we composed a "contrib-package" containing the libraries Boost, GSL, libSVM, SeqAn, glpk, zlib, bzip2 and Xerces-C.

The contrib package is contained in the OpenMS release package and is available under the path contrib in the OpenMS directory.

If you are using the developer version of OpenMS, you must check out the contrib from Sourceforge SVN repository

svn co "https://open-ms.svn.sourceforge.net/svnroot/open-ms/contrib"

CMake is used to check the system and create the contrib libraries.

  1. open a Terminal (/Applications/Terminal.app)
  2. create a build directory for the OpenMS contrib
    -e.g. $ mkdir ~/openms-development/contrib_build
  3. enter the created directory and call cmake to build the contrib

    cd <path_to_contrib_build>
    cmake <path_to_contrib>

    Example:

    cd ~/openms-development/contrib_build
    cmake ~/openms-development/contrib
    </LI>
    

If everything worked, the following sub-directories were created under in the contrib build directory:

Note
To avoid problems while building the libraries contained in the contrib package, the path to your contrib directory should not have any spaces in it.
All shipped libraries are build as Mach-O universal binaries containing both 32-bit and 64-bit x86 code.

Installing %OpenMS/TOPP

If you have not installed the libraries which %OpenMS requires,
please refer to the section @ref install_win_contrib above.
<br>
Assuming you have successfully installed the dependent libraries, you need to
get the %OpenMS source code. The latest stable version of %OpenMS
can be found in the <a href="http://www.OpenMS.de/download.php" target="_blank">download</a> page.
For further (e.g. latest developer version from SVN) info see the <a href="http://open-ms.sourceforge.net/download.php" target="_blank">download instructions</a>.
<br>
<br>
  1. open a Terminal (/Applications/Terminal.app)
  2. create a build directory for OpenMS
    -e.g. $ mkdir ~/openms-development/openms_build
  3. call cmake to create the build system there

    cd <path_to_OpenMS_build>
    cmake -D CMAKE_FIND_ROOT_PATH="<path_to_contrib_build>" <path_to_OpenMS>

    You can set CMake variables using the -D VARIABLE=VALUE option. A full list of the CMake variables is shown when you execute

    ccmake ~/openms-development/openms_build
    Note
    You need to execute cmake before using ccmake.
      Example:
    
    cd ~/openms-development/openms_build
    cmake -D CMAKE_FIND_ROOT_PATH="~/openms-development/contrib_build" "~/openms-development/openms"

The most important CMake variables are:

INSTALL_PREFIX

the path where the library is installed.
Note: Moving the library after installing it is not possible! Please use this option to point CMake to the location OpenMS should be installed to.

Install prefixes are not supported for developing with OpenMS. OpenMS must be built in place!

CMAKE_FIND_ROOT_PATH Additional search path for the contrib libraries. If not set the the location is assumed to be <path_to_OpenMS>/contrib.
QT_QMAKE_EXECUTABLE Defines the Qt 'qmake' application. The corresponding Qt installation is used.
CMAKE_BUILD_TYPE Should be either 'Release' (optimization enabled) or 'Debug' (debug info and precondition/postcondiction checks enabled).
The default is 'Release'.
QT_DB_PLUGIN Defines the Qt database type. By default MySQL is used.
CMAKE_CXX_COMPILER Defines the C++ compiler to use.

After CMake was executed, you can list the make targets by calling:

make targets

In order to build the OpenMS library and TOPP tools execute the following command:

make

If you have chosen to use a install prefix via the INSTALL_PREFIX variable you should install the components using:

make install
Note
Make sure to add <path_to_OpenMS>/lib/ (e.g. ~/openms-development/openms_build/lib/) to the environment variable DYLD_LIBRARY_PATH.
The TOPP tools are ready to use in the bin/ folder of the installation directory. Add this folder to your PATH variable.

Testing your %OpenMS / TOPP installation

After you have installed OpenMS and TOPP, you should test your installation by executing the following command:

make test_build
make test
Note
To enable DB connectivity tests, use the following CMake parameters:
  • DB_TEST
  • DB_TEST_HOST
  • DB_TEST_PORT
  • DB_TEST_DB
  • DB_TEST_USER
  • DB_TEST_PW

Building %OpenMS / TOPP with 64bit support

Building OpenMS with 64bit support requires Qt 4.5 (or higher) build with 64bit support. You need to specify the architecture, by adding the option

-D CMAKE_OSX_ARCHITECTURES="x86_64"

to the CMake call.

On Mac OS X 10.6 (Snow Leopard) 64bit is the default architecture. Use

-D CMAKE_OSX_ARCHITECTURE="i386"

to create a 32bit binary.


OpenMS / TOPP release 1.9.0 Documentation generated on Sun Oct 27 2013 01:11:37 using doxygen 1.8.4