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Laurent Guéguen edited this page Jun 4, 2025 · 12 revisions

How to install Bio++.

Table of Contents

Lastest release : Bio++ 3.0.0

Ubuntu/Debian packages

Bio++ 3.0 packages (libbpp-core, libbpp-seq, etc.) are available in the Debian Testing repositories (and are subsequently transferred to Debian Stable and Ubuntu). They can be installed using your usual package/program manager.

MacOS X

The Bio++ libraries and program are available from Homebrew. You need to add the corresponding tap with the command brew tap jydu/homebrew-biopp Each library is available as libbpp-core, libbpp-seq, etc. together with the bppsuite programs.

Apptainer

An apptainer image of all libraries and binaries of bpp (including testnh) is available on pbil.

An easy way to use this container is to open a shell in it, and then all binaries are available:

apptainer shell bpp.sif

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

libbpp-phyl depends on Eigen3 (version >= 3.8). Ensure it is installed at standard location.

Development version

git and CMake are needed to retrieve and compile the source files. They can be installed through the git and cmake 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 : 

git
cmake

Installing Bio++ in a custom location greatly helps in compiling and running different programs depending on different Bio++ versions. This section therefore shows how to download the sources in directory $HOME/devel/bpp and install the libraries in $HOME/.local/lib and $HOME/.local/bin.

Setting up the source direcory

We start by creating the directory : 

PROJECTDIR=$HOME/devel/bpp/
mkdir -p $PROJECTDIR/
cd $PROJECTDIR/

Getting the source files

This is done with git. Git repository is available from GitHub.

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 and bpp-phyl.) 

cd $PROJECTDIR
git clone https://github.com/BioPP/bpp-core
git clone https://github.com/BioPP/bpp-seq
git clone https://github.com/BioPP/bpp-popgen
git clone https://github.com/BioPP/bpp-phyl
git clone https://github.com/BioPP/bppsuite

At this point the $HOME/devel/bpp directory should contain five 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) : 

cd bpp-core
mkdir build
cd build
cmake -B . -S .. -DCMAKE_INSTALL_PREFIX=$HOME/.local # prepare compilation
make # compile
make install # move files to the installation directory

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

Notes

  • Environment. 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:
export CPATH=$CPATH:path_to_the_library/include    # for compilation
export LIBRARY_PATH=$LIBRARY_PATH:path_to_the_library/lib    # for compilation
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:path_to_the_library  # for execution
  • Debugging symbols. Usage of a debugger is possible if the option -D CMAKE_BUILD_TYPE=Debug is added to the cmake command line.
  • On some systems, 64-bits libraries have to be installed in lib64/ directories instead of just lib/. This can be achieved by passing the -DLIB_SUFFIX=64 option to cmake.

Staying up-to-date

To update the libraries the basic procedure is : 

cd bpp-core
git pull # retrieve changes
cd build
cmake ./ # update files list
make
make install

Alternatively, the following script can be used : 

#!/bin/bash

cd $PROJECTDIR
for d in bpp-core bpp-seq bpp-phyl bpp-popgen bpp-raa bpp-qt; do
  if [[ ! -e $d ]]; then
    echo -e "Skip $d (does not exist).\n"
    continue
  fi
  
  echo "Updating $d..."
  cd $d/
  git pull
  cmake .
  if make; then
    echo "Installing..."
    make install >/dev/null
  else
    echo "Compilation error in '$d/'. Abort"
    cd ..
    break
  fi
  cd ..
done
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