GitHub - BioPP/bppsuite: Bio++ Program Suite (original) (raw)

BppSuite presentation

BppSuite is a suite of ready-to-use programs for phylogenetic and sequence analysis.

Installation

From source files

Get the sources

This is done with git, for example in directory $bpp_dir:

cd $bpp_dir git clone https://github.com/BioPP/bppsuite

Compiling

Bio++ libraries need to be installed beforehand, for example in $bpp_dir. The needed libraries are bpp-core, bpp-seq, bpp-phyl, bpp-popgen. See installation for instructions.

After, you proceed:

cd bppsuite cmake -DCMAKE_INSTALL_PREFIX=$bpp_dir ./ # prepare compilation make # compile make install # move files to the installation directory (this will create a $bpp_dir/bin/ directory)

That's it ! The executables are now installed in $bpp_dir/bin.

Without the option -DCMAKE_INSTALL_PREFIX=$bpp_dir, the standard /usr/local directory will be used, and the executables installed in /usr/local/bin, a location which requires superuser access rights.

Containers

Bppsuite and testnh are available in a singularity container, there.

Usage

Bppsuite executables should know where the dynamic libraries are. A way to check it is the command:

ldd bppdirbpp_dirbppd​ir/bin/bppml

To configure this, set in the shell environment variable :

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$bpp_dir

(and source the configuration file or relog).

Documentation

You can generate the pdf documentation by typing :

make pdf

and in html by typing:

make html

Examples

Many examples are available in the subdirectory of Examples.

Documentation

Documentation can be found at: https://pbil.univ-lyon1.fr/bpp-doc/bppsuite/bppsuite.html