Installation

Orthoflow can be installed using conda, PyPI or from source.

Conda Installation

To install with conda, use the following command:

conda install -c bioconda orthoflow

pip Installation

Orthoflow can be installed with pip from the Python Package Index (PyPI) as follows.

pip install orthoflow

Orthoflow can also be installed directly from Github using pip as follows.

pip install git+https://github.com/rbturnbull/orthoflow.git

Note

If installing with pip, conda needs to be available on the system for the workflow to run.

Source Installation

To install from the source code, first ensure that the dependency manager poetry is installed on the system. You can install the latest version of poetry on Mac and Linux like this:

curl -sSL https://install.python-poetry.org | python3 -

On windows, it can be installed with this command:

(Invoke-WebRequest -Uri https://raw.githubusercontent.com/python-poetry/poetry/master/get-poetry.py -UseBasicParsing).Content | python -

Then clone the orthoflow repository from github:

git clone https://github.com/rbturnbull/orthoflow.git
cd orthoflow

Install the code into a virtual environment managed by poetry as follows:

poetry install

Enter into the virtual environment as follows:

poetry shell

Note

If installing from source, conda needs to be available on the system for the workflow to run.