Installation

Install MONSDA via conda or pip

To install via conda/mamba in an environment named ‘monsda’ simply run

conda create -n monsda -c bioconda -c conda-forge monsda

To install via pip you first need to create the MONSDA environment as found in the envs directory of this repository (simply clone with git clone) like so:

conda env create -n monsda -f MONSDA/envs/monsda.yaml

The envs directory holds all the environments needed to run the pipelines in the workflows directory, these will be installed automatically alongside MONSDA.

For that activate the MONSDA environment and run pip

conda activate monsda
pip install MONSDA

Install from source

Simply clone this repository with

git clone git@github.com:jfallmann/MONSDA.git

You can then install dependencies as described for pip installation and manually run setup.py.

Be aware that MONSDA is version dependent, so config files can only be run with the specified version of MONSDA in order to guarantee reproducibility by conserving dependencies and environments.