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.