Installation
------------

.. admonition:: Under construction

    The package is under construction, therefore the pip and container installations might be lagging behind.
    Clone the main branch from the repository to use the most up to date stable version corresponding to the documentation.

You can either install from `pypi <https://pypi.org/project/inMOTIFin/>`_ with the command

``python -m  pip install inmotifin``

or pull the container at `dockerhub <https://hub.docker.com/r/cbgr/inmotifin/tags>`_. If you have `docker <https://www.docker.com/>`_ installed, you can run from within the docker container with

``sudo docker run -it cbgr/inmotifin:3.0.3 bash``

When using the pip install, you may want to create a conda environment for it.
The commands below will do that for you:

.. code-block:: bash

    conda create --name inmotifin python=3.10
    conda activate inmotifin
    python -m  pip install inmotifin


Altenarively, you can also clone `the inMOTIFin bitbucket repository <https://bitbucket.org/CBGR/inmotifin/src/main/>`_ and install the package locally by ``pip install -e .`` run in the folder where the ``setup.py`` file resides.

============
Dependencies
============

The code is written in python 3.9 .
The following dependencies are installed with the software

* `click <https://click.palletsprojects.com/en/stable/>`_
* `numpy <https://numpy.org/>`_
* `pandas <https://pandas.pydata.org/>`_
* `DagSim <https://uio-bmi.github.io/dagsim/quickstart.html>`_
* `pyjaspar <https://github.com/asntech/pyjaspar>`_
* `biopython <https://biopython.org/>`_
* `hmmlearn <https://hmmlearn.readthedocs.io/en/latest/>`_