Installation

Environment setting

We recommend to create a separated conda environment for running BRIE2, which heavily depends on TensorFlow and TensorFlow-probability.

conda create -n TFProb python=3.7

replace -n TFProb with -p ANY_PATH/TFProb to specify the path for conda environment. Then activate the environment by conda activate TFProb or the full path, before install more packages.

Easy install

BRIE2 is available through pypi. To install, type the following command line, and add -U for upgrading:

pip install -U brie

Alternatively, you can install from this GitHub repository for latest (often development) version by following command line

pip install -U git+https://github.com/huangyh09/brie

In either case, if you don’t have write permission for your current Python environment, add --user, but check the previous section on create your own conda environment.

GPU usage

With TensorFlow backend, BRIE2 can benefit from using GPUs. Here is one way to set up GPU configurations with NVIDIA GPU on Ubuntu:

pip install -U tensorflow-gpu
conda install -c anaconda cupti
conda install -c anaconda cudnn
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/extras/CUPTI/lib64

For more information on GPU configuration, please refer to the Tensorflow documentation, or anaconda GPU.

Note

At the moment, TensorFlow calls all available GPUs, which is not nessary. You can specify the card you want to use by add the following variable before you command line CUDA_VISIBLE_DEVICES=3 brie-quant -i my_count.h5ad

Test

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

Welcome to brie-quant in BRIE v2.0.2!

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-quant: 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"

If you have any issue, please report it to the issue on brie issues.