Installation

How to install Bio++.

See also Bio++ Versions

See also Installation (old page).

Ubuntu/Debian packages
Bio++ 2.1 packages (libbpp-core, libbpp-seq, etc.) are available in the Ubuntu and Debian standard repositories. They can be installed using your usual package/program manager.

Warning: as of June 30, 2012, there is an issue with the Ubuntu popgen package. If you want to use this part of the library, please use the package from the custom repository instead, or compile from source, or switch to the development version.

Packages for version 2.2.0. have not been uploaded yet, and are only available from the custom repository.

Ubuntu/Debian packages (custom repository)
A local repository is available for architectures i386 and amd64, containing additional programs built against the libraries.

Use your favorite apt manager to add the following line to your sources.list :

deb http://biopp.univ-montp2.fr/repos/apt/ Trusty main

You will also need to add the key that was used to sign the packages :

Reload the packages list and then look for "Bio++" packages. That's all!

Packages are built with an Ubuntu system. Here are the version correspondences:

Make sure to use the appropriate distribution name in your 'source.list'.

RPM packages
RPM packages (version >= 2.0.3) are available at http://download.opensuse.org/repositories/home:/jdutheil:.

Additional RPMs for Mageia 4 are available at http://biopp.univ-montp2.fr/repos/rpm/RPMS/x86_64/mga4/.

MacOS X
DMG packages are available at http://biopp.univ-montp2.fr/repos/dmg/ (compiled with a MacIntel computer).

Compiling from source
Compiling from source is necessary when superuser rights are not available or to install Bio++ to a non-standard location (useful when several Bio++ versions coexist on a system).

automatically
The easiest way to compile from source is to download the Bio++ automatic installer, edit the script header to match your system, and run it.

For instance, to download the sources in $HOME/local/bpp/latest/sources and install the libraries in $HOME/local/bpp/latest/lib and $HOME/local/bpp/latest/include, one would enter :

manually
Download the source archives individually. The compilation and installation procedure is then the same as for compiling the development version.

Development version
git and CMake are needed to retrieve and compile the source files. They can be installed through the git and cmake</tt> packages in Ubuntu/Debian repositories, and should be present on most servers. You can check whether they are installed on your system simply by typing :

Installing Bio++ in a custom location greatly helps in compiling and running different programs depending on different Bio++ versions. This section therefore demonstrates how to download the sources in $HOME/local/bpp/dev/sources</tt> and install the libraries in $HOME/local/bpp/dev/lib</tt> and $HOME/local/bpp/dev/include</tt>.

We start by creating the directory :

Getting the source files
This is done with git</tt>. Git repository is available from GitHub.

You need to download only the components of the library that you want to use. The bpp-core</tt> and bpp-seq</tt> components are required by all others, which are otherwise independent. (Example is given for bpp-popgen</tt> and bpp-phyl</tt>.)

At this point the sources</tt> directory should contain three subdirectories.

Compiling and installing
All desired components must be compiled and installed successively, starting with bpp-core</tt> and bpp-seq</tt>. Repeat the following steps (example given for bpp-core</tt>) :

That's it ! The libraries are now installed. For more information on how to compile and run Bio++ dependent programs, see the Usage pages.

Explanation : CMake can be given internal variables using the -D</tt> option. The install directory is specified by the CMake CMAKE_INSTALL_PREFIX</tt> variable. Because our install directories are non-standard (eg. not /usr/local/lib</tt>), the CMake <tt>CMAKE_LIBRARY_PATH</tt> and <tt>CMAKE_INCLUDE_PATH</tt> variables must also be provided (this is actually dispensable for <tt>bpp-core</tt> given that it does not depend on the other components).

Staying up-to-date
To update the libraries the basic procedure is :

Alternatively, the following script can be used :

Older versions
Former versions of libraries and API documentation are available from here. Browsable documentation is only available for the previous release of Bio++. Older documentation must be downloaded.

Installing a previous version of the libraries is necessary when maintaining or modifying programs that depend on those libraries. The preferred procedure is to compile from sources. From version 1.9, the installation procedure is the same as for the development version. Source files can be found at http://biopp.univ-montp2.fr/repos/sources/.

Bio++1.8
Note that version 1.8 uses autotools.