installation
============


Download:
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dmr_analysis is written in python. It can be installed and accessed from command line and is available for both linux and mac operating systems. The package can be downloaded `here <https://github.com/dmr-analysis/dmr_analysis/archive/refs/heads/master.zip>`_ . Or type command:

.. code-block:: bash

    wget https://github.com/dmr-analysis/dmr_analysis/archive/refs/heads/master.zip

Please send email to Dr. Junbai Wang (junbai.wang@medisin.uio.no) for requesting a free download of full DMR-analysis pacakge.

Please include your name, Institution/company name, Email of your institute or company (do not use gmail or yahoo email etc), and a brief description of the purpose for using bpb3 package.

Please use the subject title "bpb3/dds/dmr request "  for your email.


Install:
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It is highly recommended to create a separate virtual environment for the package to avoid any library conflicts problem. You can create a virtual environment using the following commands. We recommend installing and using miniconda/anaconda (`https://docs.conda.io/en/latest/miniconda.html`). Tutorial of creating and updating virtual commands can be found at (`https://conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html`).

If miniconda is already installed, then you can proceed with the following step-by-step installation. We have already provided a quick installation setup file named ``quick_install.sh`` for your ease. A simple bash command will do everything automatically and prepare the package, ready to run.

.. code-block:: bash

    ./quick_install

However, step-by-step details are given as under and can be followed if ``quick_install.sh`` is unsuccessful:

.. code-block:: bash

    conda create --name dmr_env python==3.9.16
    conda activate dmr_env

Install pip if not already installed:

.. code-block:: bash

    conda install pip

Please allow any other installations when prompted.

Requirements:
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Prior to installing the package, dependencies must be fulfilled. It is advised to install dependencies using miniconda. The list of dependencies is as follows:

- matplotlib==3.5.3
- numpy==1.21.5
- pandas==1.4.4
- scikit_learn==1.2.2
- scipy==1.9.1
- setuptools==65.6.3
- statsmodels==0.13.5
- bedtools==2.27.0

These dependencies can be installed one by one using the conda manager. For example:

.. code-block:: bash

    conda install numpy==1.21.5

A ``requirements.txt`` file is given with the package. All requirements can be automatically installed using one command:

.. code-block:: bash

    conda install --file requirements.txt

Or they can be installed using pip.

.. code-block:: bash

    pip install numpy==1.21.5

A ``requirements.txt`` file is given with the package. All requirements can be automatically installed using one command:

.. code-block:: bash

    pip install -r requirements.txt

You can install the package using the following command. Go to the dmr_analysis directory (folder containing setup.py and pyproject.toml) and type the following command:

.. code-block:: bash

    pip install .

For more details, follow the readme file in the package.