Installation

The following sections describe how to install the scflow framework.

Conda Installation

The preferred method for installation is through conda. Currently this installation is still in working progress. Preferably the installation should be in a separate environment.:

# The conda environment is currently not ready but we are working on this
#conda create -n scflow -c cgat scflow
#conda activate scflow
#scflow --help

Pip installation

You can install scflow using pip, this will only install the package without any dependancies, which will have to be installed separately.:

pip install scflow

Manual Installation

The repository can also be installed manually, but dependancies will need to be installed separately.:

git clone https://github.com/Acribbs/scflow.git
python setup.py install
scflow --help

Installing additional software

We always recommend using conda to install additional software where possible.

This can be easily performed by:

conda search <package>
conda install <package>