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This document addresses OpenMS users and explains the installation procedure. It 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). All installations are explained from sources, but you should consider using precompiled packages suited for your system.
Required applications
In order to compile OpenMS, several applications need to be installed:
-
Compiler: An ANSI-compatible C++ compiler is required.
We recommend to use g++ 4.1.0 or higher.
g++ is part of the GNU Compiler Collection (GCC).
-
Autoconf 2.9 or higher is required
-
GNU make is required
If your OpenMS version is a development version from SVN, the following applications are needed in order to create the OpenMS documentation:
-
doxygen (We recommend version 1.4.5 or higher)
-
pdflatex
OpenMS depends on several other libraries. Most of them are standard and should be present in many systems anyway. Some of those libraries again depend on others. Here is a little overview of the dependencies:
| ANDI/MS | (requires NetCDF) |
| GSL | |
| CGAL | |
| XERCES-C | |
| libSVM | |
| Qt | (requires other libraries for DB support e.g. MySQL) |
In order to make the installation of the required libraries easier, we composed a "contrib-package" containing the libraries ANDI/MS, NetCDF, GSL, CGAL, libSVM and XERCES-C. This contrib package has several advantages over manual installation
-
you get all the libraries in versions tested with OpenMS.
-
it contains a configure script that builds all the libraries in one step.
-
you don't have to spend hours reading installation instructions of all the libraries.
-
we applied some patches to the libraries to fix some bugs.
These bugs may be fatal if you do not use the contrib package.
We recommend using the contrib package! Qt and MySQL are not contained in the contrib package as they are installed on most systems anyway. If they are not installed on your system, you have to install those two libraries first.
The MySQL database is accessed by OpenMS through functionality provided by Qt. The MySQL versions 4.0.18 and 4.1.10a have been tested and used with OpenMS.
You can get the sources at http://dev.mysql.com/downloads/mysql/4.1.html in the 'source download' section.
Good installation instructions for MySQL can be found at http://dev.mysql.com/doc/mysql/en/installing-source.html.
Basically the installation boils down to this:
> ./configure --prefix=<prefix>
> make
> make install
- Note:
- If you want to use preinstalled MySQL binaries, make sure that the mysql-devel package is installed.
For GUI and database access we use Qt 4.2 or higher. You can obtain the source code from http://www.trolltech.com/download/index.html.
Run configure with the '-verbose' option. With that option a summary is shown before the you have to accept the licence. Make sure that MySQL (or any other DB you want to use) and OpenGL support are enabled in the summary.
> ./configure -verbose -fast -no-qt3support (... see below)
> make
SQL support:
Use the configure option '-qt-sql-<driver>' to enable database support. There is a Qt driver for a lot of SQL database provided by Qt. Check the Qt manual for details.
- Note:
- If you want to use the preinstalled binaries, make sure that the qt-devel package is installed.
First download the contrib package (you can find the contrib package here).
Alternatively you can check out the contrib from Sourceforge SVN repository > svn co https://open-ms.svn.sourceforge.net/svnroot/open-ms/contrib
to obtain the latest developer version (potentially unstable).
Now do:
> autoconf
> ./configure
The following configure options can be used:
| --with-compiler=CXX | use CXX as C++ compiler (default: g++) |
| --with-c-compiler=CC | use CC as C compiler (default: gcc) |
If you do not give any configure options, it is assumed that you want to use 'gcc' as C-compiler and 'g++' as C++-compiler.
Next you can build all the libraries with
> make
If everything worked, the following sub-directories were created:
-
'lib/' or the given 'libdir' (as ./configure option)
It contains the libraries needed by OpenMS.
This directory should be added to your LD_LIBRARY_PATH variable.
-
'include/'
It contains the header files needed for OpenMS.
In order to point the OpenMS configure to the contrib libraries you can use the configure option '--with-default-path'. The default value of this option is 'OpenMS/contrib/' so you can move the contrib package there to make OpenMS find it automatically.
If you have not installed the libraries which OpenMS requires, please refer to the section Installing required dependency libraries above. Otherwise you might only get parts of the full OpenMS functionality.
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 files section. For further (e.g. latest developer version from SVN) info see the download instructions.
After you got the source code go to the source
directory and type in the following commands (... see 'configure --help' and below for more options during ./configure
)
> ./configure
> make
> make install
This should do the job.
The most important configure options are:
--prefix=DIR | the path where the library is installed.
Note: Moving the library after installing it is not possible! Please use this option to point configure to the location OpenMS should be installed to. |
--with-default-path=DIR | use default path DIR/include for header files and DIR/lib for libraries (../contrib if unset) |
--with-qt=QTDIR | Qt is installed in QTDIR. |
--with-compiler=CXX | use CXX as C++ compiler |
- Note:
- If
./configure
is not executable on your system, you should execute autoconf
before the above commands.
If ./configure
fails, a file called config.diag.tar is created. Please send this file together with a description of the problem by email.
Add <path_to_OpenMS>/lib/ (e.g. ~/OpenMS/lib/) to the environment variable LD_LIBRARY_PATH (as suggested by the previous make
).
After you have installed OpenMS, you can test your installation by executing the following command:
> cd <path_to_OpenMS>/source/
> make test
- Note:
- To test the DB connectivity, copy the file '<path_to_OpenMS>/source/TEST/DB_credentials_template.txt' to 'DB_credentials.txt' and fill in your DB access details. As long as the 'DB_credentials.txt' file remains there, the DB will be tested with any subsequent call of 'make test'. In order to successfully test DB connectivity, the database must exist and the the given user must have write access to the database.
If ANDI/MS (cdf) tests fail, you can disable ANDI/MS (cdf) support using --disable-andims
in the OpenMS configure.
TOPP is a toolset for the analysis of HPLC/MS data. It consists of several small applications that can be chained to create analysis pipelines tailored for a specific problem.
After you have built OpenMS, you can build the TOPP tools with the following command:
> cd <path_to_OpenMS>/source/
> make TOPP
Now the TOPP tools are ready to use in ${PREFIX}/bin/
.
After you have built the TOPP tools, you can test them with the following command:
> cd <path_to_OpenMS>/source/
> make TOPPtest
- Note:
- To test the DBImporter and DBExporter go to the '<path_to_OpenMS>/source/TEST/TOPP/' directory and copy the files 'DBImporter_input_template.ini' and 'DBExporter_input_template.ini' to 'DBImporter_input.ini' and 'DBExporter_input.ini', respectively. Then fill in your DB access details. As long as these file remains there, the DB will be tested with any subsequent call of 'make TOPPtest'. In order to successfully test the tools, the database must exist and the the given user must have write access to the database.
Generated Tue Apr 1 15:36:40 2008 -- using doxygen 1.5.4 |
OpenMS / TOPP 1.1 |