Installation

From Bio++ Wiki
Jump to: navigation, search

How to install Bio++. See also Installation (old page).

Lastest version : Bio++ 2.0

Ubuntu/Debian packages

Bio++ 2.0 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.

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/debian Squeeze main

You will also need to add the key that was used to sign the packages : <source lang="bash"> wget http://biopp.univ-montp2.fr/repos/apt/conf/biopp.gpg.key sudo apt-key add biopp.gpg.key </source>

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

RPM packages

RPM packages are available at http://download.opensuse.org/repositories/home:/jdutheil:/Bio++/.

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).

Remark: CMake is needed to compile the sources (cmake package in Ubuntu/Debian repositories).

Compiling from source : the automatic way

The easiest way to compile from source is to download the 2.0 automatic installer, edit the script header to match your system, and run it.

For instance, to download the sources in $HOME/local/bpp2.0 and install the libraries in $HOME/local/lib and $HOME/local/include, one would enter : <source lang="bash"> mkdir $HOME/local $HOME/local/bpp2.0 cd $HOME/local/bpp2.0 wget http://biopp.univ-montp2.fr/Download/bpp-setup.sh chmod +x bpp-setup.sh gedit bpp-setup.sh # set PATH_INSTALL to $HOME/local/, on line 16 ./bpp-setup.sh </source>

Compiling from source : the manual way

Download the source archives individually (see Bio++ Versions). The compilation procedure is then the same as for compiling the development version.

Development version

Remark: git and CMake are needed to download and compile the source files (git and cmake package in Ubuntu/Debian repositories).

Remark: Installing Bio++ in a custom location greatly helps in compiling and running programs depending on different Bio++ versions. This section demonstrates how to download the sources in $HOME/local/bpp/dev/sources and install the libraries in $HOME/local/bpp/dev/lib and $HOME/local/bpp/dev/include. For more information on how to compile/run Bio++ dependent programs, see the Usage pages.


We start by creating the directory : <source lang="bash"> bpp_dir=$HOME/local/bpp/dev/ mkdir -p $bpp_dir/sources </source>

Getting the source files

This is done with git.

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

<source lang="bash"> cd $bpp_dir/sources git clone http://biopp.univ-montp2.fr/git/bpp-core git clone http://biopp.univ-montp2.fr/git/bpp-seq git clone http://biopp.univ-montp2.fr/git/bpp-popgen </source>

At this point the sources directory should contain four subdirectories.

Compiling and installing

All desired components must be compiled and installed successively, starting with bpp-core and bpp-seq. Repeat the following steps (example given for bpp-core) : <source lang="bash"> cd bpp-core cmake -D CMAKE_INSTALL_PREFIX=$bpp_dir -D CMAKE_LIBRARY_PATH=$bpp_dir/lib -D CMAKE_INCLUDE_PATH=$bpp_dir/include . # prepare compilation make # compile make install # move files to the installation directory </source>

That's it !

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

Remark: If Bio++ libraries are already present on your system, CMake will issue a warning because this interferes with the compilation of the testing executables (but not with that of the libraries). Remove the CMakeCache.txt file and specify -D BUILD_TESTING=FALSE on the cmake command to tell CMake to skip the compilation of those executables.

Older versions

See Bio++ Versions.