Installation (old page)

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Installing pre-compiled version of Bio++

Linux

Pre-compiled distribution come as two flavors: rpm (RedHat Package Manager) and deb (Debian) packages, for 32 and 64 bits architectures. You can download the packages individually from the repository (see [1]), or configure your system to automatically fetch them (debian only).

You can find several type of packages:

  • Packages for compiled program use,
  • Packages for development and compilation of programs,
  • Source packages (rpm only).

The last category is equivalent to the .tar.gz distribution. The first one provides the dynamic libraries, and is for using program developed using Bio++ and compiled dynamically. The second category is for developing or compiling a program with Bio++. It provides the static libraries and header files. It depends on the packages of the first category.

RPM packages are then installed using the command <source lang="bash"> rpm -i libbpp-XXXXX.deb </source> and DEB packages using the command <source lang="bash"> dpkg -i libbpp-XXXXX.deb </source> You will need root access to execute these commands. To install Bio++ locally, you have to install from sources.

MacOsX

DMG packages are available there [2] (compiled with a MacIntel computer).

Installing Bio++ from source files: the automatic way

This uses an installation file written in bash. start by dowloading it at [3] in a empty directory, and make it executable: <source lang="bash"> chmod +x bpp-setup.sh </source> The launch it <source lang="bash"> ./bpp-setup.sh </source> On some systems (Sun for instance), you may need to type <source lang="bash"> . ./bpp-setup.sh </source> instead. The script will check you have all required tools in the right place, download the sources, unpack, configure, compile and install them!

Note: Be sure to have the write access for the installation directory you chosed! In some cases, you will have to run it as super-user.

Installing Bio++ from source files: the manual way

Installation from source files is possible under Linux-like systems (Linux, Unix, MacOS X, CygWin).

Get the source files

Current version using the Version System (Git)

  • Get yourself into the directory where you want the project files to be.

Each library will come in a separate directory.

  • Then retrieve the libraries you need:

<source lang="bash"> 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 git clone http://biopp.univ-montp2.fr/git/bpp-raa git clone http://biopp.univ-montp2.fr/git/bpp-qt </source>

Archives from the source distribution (targz)

Archives of Bio++ are distributed via a bundle of source file archives on its website, [4].

  • Download and copy the distribution (.tar.gz files) into a directory where you have writing rights,
  • Decompress each archive file with the command

<source lang="bash"> tar xvzf archive.tar.gz </source>

Compiling and installing under Linux-like systems

From now, repeat the following steps for each library in the following order:

  • bpp-core
  • bpp-seq
  • bpp-phyl (optional)
  • bpp-popgen (optional)
  • bpp-raa (optional)


  • <source lang="bash">cd</source> to the source directory,
  • build the Makefile with cmake

<source lang="bash"> cmake . </source> The libraries will be installed in /usr/local, a location which requires superuser access rights. An alternative option consists in installing in the user home, for example in a subdirectory called .local. <source lang="bash"> cmake . -DCMAKE_INSTALL_PREFIX=$HOME/.local </source> The CMAKE_INSTALL_PREFIX variable specifies where the libraries should be installed. See Note 2 below.

  • Build the library: <source lang="bash">make</source>
  • Then install it: <source lang="bash">make install</source>
  • You can also generate the API documentation by typing <source lang="bash">make apidoc</source>

Notes

  • When installing the other libraries, if you have several versions of the libraries on your system (for instance one in /usr/local/ in addition to your own in $HOME/.local, you can tell cmake which version to link to by running

<source lang="bash"> cmake . -DCMAKE_INSTALL_PREFIX=$HOME/.local </source>

  • If you install lour libraries in a non standard directory, you should tell where the dynamic libraries are. For example, with bash shell, you can add in your .bashrc:

<source lang="bash"> export CPATH=$HOME/.local/include # for compilation export LIBRARY_PATH=$HOME/.local/lib # for compilation export LD_LIBRARY_PATH=$HOME/.local # for execution </source>

  • If you are updating a library and encounter compatibility problems for test programs, you should add the option -DBUILD_TESTING=OFF

so that new libraries are installed without any compilation of the test programs.

  • Usage of a debugger is possible if the option -DCMAKE_BUILD_TYPE=Debug is added to the cmake command line.
  • On some 64bits systems, 64-bits libraries have to be installed in lib64 instead of lib. This can be achieved by passing the -DLIB_SUFFIX=64 option to cmake.