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.