Difference between revisions of "Installation"

Revision as of 20:22, 7 December 2017

How to install Bio++.

Lastest release : Bio++ 2.3.1

Ubuntu/Debian packages

Bio++ 2.3 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.

RPM packages

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

SlackWare linux

Bio++ / BppSuite 2.3 is available in SlackBuild (thanks to Petar Petrov), see https://slackbuilds.org/repository/14.2/academic/bpp-core/.

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.

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.

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 : <source lang="bash"> git cmake </source>

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 and install the libraries in $HOME/local/bpp/dev/lib and $HOME/local/bpp/dev/include.

We start by creating the directory :

bpp_dir=$HOME/local/bpp/dev/
mkdir -p $bpp_dir/sources

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 $bpp_dir/sources
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

At this point the sources directory should contain three 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
cmake -DCMAKE_INSTALL_PREFIX=$bpp_dir . # 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
cmake ./ # update files list
make
make install

Alternatively, the following script can be used :

#!/bin/bash

cd $HOME/local/bpp/dev/sources
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

Older versions

See also Installation (old page).

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++1.9

wget http://biopp.univ-montp2.fr/repos/sources/bpp-utils-1.5.0.tar.gz
wget http://biopp.univ-montp2.fr/repos/sources/bpp-numcalc-1.8.0.tar.gz
wget http://biopp.univ-montp2.fr/repos/sources/bpp-seq-1.7.0.tar.gz
wget http://biopp.univ-montp2.fr/repos/sources/bpp-phyl-1.9.0.tar.gz
wget http://biopp.univ-montp2.fr/repos/sources/bpp-popgen-1.5.0.tar.gz

Bio++1.8

wget http://biopp.univ-montp2.fr/repos/sources/bpp-utils-1.4.0.tar.gz
wget http://biopp.univ-montp2.fr/repos/sources/bpp-numcalc-1.7.0.tar.gz
wget http://biopp.univ-montp2.fr/repos/sources/bpp-seq-1.6.0.tar.gz
wget http://biopp.univ-montp2.fr/repos/sources/bpp-phyl-1.8.0.tar.gz
wget http://biopp.univ-montp2.fr/repos/sources/bpp-popgen-1.4.0.tar.gz

Note that version 1.8 uses autotools.