How to install Bio++. See also Installation (old page).
- 1 Lastest version : Bio++ 2.0
- 2 Development version
- 3 Older versions
Lastest version : Bio++ 2.0
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 are available at http://download.opensuse.org/repositories/home:/jdutheil:/Bio++/.
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.
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 do not need to download all components of the Bio++ library. Namely, the bpp-core and bpp-seq components required by all others, which are otherwise independent.
<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-phyl git clone http://biopp.univ-montp2.fr/git/bpp-popgen </source>
At this point our sources directory should contain four subdirectories.
Compiling and installing
All desired components must be compiled successively.
See Bio++ Versions.