Installation

Anaconda

For first-time conda users, perform a one-time set up of Bioconda with the following commands:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda config --set channel_priority strict

To install simba with conda, run:

conda install -c bioconda simba

Recommended: install simba in a new virtual enviroment:

conda create -n env_simba simba
conda activate env_simba

Dev version

To install the latest version on GitHub,

first install simba_pbg

conda install -c bioconda simba_pbg

then run:

git clone https://github.com/huidongchen/simba.git
pip install simba --user

or:

pip install git+https://github.com/huidongchen/simba