Note: See Create a new conda environment in tutorial, to learn how to install pyrpipe and required tools in an conda environment.

Before installing pyrpipe, make sure conda channels are added in right order

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

pyrpipe is available through bioconda could be installed via:

conda install -c bioconda pyrpipe

pyrpipe is available on PyPI and could be installed via pip:

pip install pyrpipe

To install from source, clone the git repo:

git clone

Then install using pip:

pip install -r pyrpipe/requirements.txt
pip install -e pyrpipe

To run tests using pytest, from the pyrpipe root perform:

py.test tests/<specific test file>