Installation

Easy install

  • Required packages in python: numpy, matplotlib, pysam, h5py

    • we suggest using Anaconda distribute, which includes most packages (except pysam here), and provides you a user specific environment, i.e., all your python packages go to a single folder. Thus, you don’t need the root to install packages.
    • you could install pysam by pypi in terminal, or download and install it in the same way as BRIE.

  • You can install BRIE simply via pypi in terminal (suggested), or upgrade by add --upgrade as follows:

    pip install brie

pip install --upgrade --no-deps brie

Source code

  • Alternatively, you also could download the source code via GitHub (latest version, suggested) or Sourceforge (any version) and run python setup in terminal:

    python setup.py install

  • In any case, if had the permission error for installation as you are not root, add --user.

Test

In order to test the installation, you could type brie. If successful, you will see the following output.

Welcome to Brie!

use -h or --help for help on argument.

If installation is sucessful, but can’t run it, then check whether the directory which contains the executable binary file is added to PATH environment.

brie: command not found

Usually the directory is ~/.local/bin if you don’t use Anaconda. You could add the path into PATH environment variable, by write the following line into .profile or .bashrc file.

export PATH="~/.local/bin:$PATH"