.. _install:


Installation
============

Install MONSDA via **conda** or **pip**
-------------------------------------------

To install via **conda/mamba** in an environment named 'monsda' simply run

.. code-block::

    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:

.. code-block::

    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**

.. code-block::

    conda activate monsda
    pip install MONSDA


Install from source
-------------------

Simply clone this repository with 

.. code-block::
    
    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.