Installation

This page will guide you through the installation process. Let’s have a look at the requirements first.

Note

Be aware that in the programs of DomainWorld, the BioSeqDataLib is usually included as a submodule and you don’t have to manually download it unless you have no internet connection and/or don’t want to use git. Compilation will not be needed if you use it with the programs provided on this website.

Requirements

We try to keep the dependencies as little as possible. Current dependencies are:

cmake (https://cmake.org)
compiler supporting c++11 - e.g. g++ 4.8 or higher
boost modules: system, filesystem and iostreams (http://www.boost.org/)

Optional:

git (https://git-scm.com/)- Recommended: It simplifies future update processes
boost modules: unit_test - only needed when unit_tests should be compiled

In most Linux distributions (e.g. Ubuntu, Arch Linux) it should be possible to install these dependencies using the package manager.

Download

You can either download the compressed source code from our gitlab webpage https://zivgitlab.uni-muenster.de/domain-world/BioSeqDataLib or use git to clone the repository:

git clone https://zivgitlab.uni-muenster.de/domain-world/BioSeqDataLib.git

Tip

If you use ‘git clone’ you can easily update to a newer version when available.

Compilation & Installation

If you want to use the library as a shared library follow the instructions below to compile and install it. Create a build directory inside the source folder in which the code will be compiled. CMake is used to find all the needed requirements of the library.

mkdir build
cd build
cmake ..
make

To install type the command below. However, you will need root rights for it.

sudo make install

You probably need to set up some parameters in a configuration file but don’t worry that is easy to do. Have a look here

Updating

Sometimes it will be necessary to update the BSDL if you install a new version of a program either because it contains some new features or because we unfortunately had a bug somewhere that we have now fixed. If you used git for the original download you can simply use git to update your code. Simply change into the BioSeqDataLib directory and type:

git pull

You now simply follow again the steps in the Installation section. If you downloaded the code without git you will have to download the latest version and replace the old one with it.