Install STRonGR
===============

In order to install STRonGR, you will need to follow the steps described below.

Install Conda
-------------

In order to install Conda, please follow the official `Conda installation instructions <https://docs.continuum.io/anaconda/install/>`_.

This will likely be something like this:

.. code-block:: sh
  :linenos:

  # Conda pre-requisites
  apt-get install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6

  # Download latest conda installer
  wget https://repo.anaconda.com/archive/Anaconda3-2019.03-Linux-x86_64.sh

  # Run the installer
  bash ~/Downloads/Anaconda3-2019.03-Linux-x86_64.sh


Create Conda environment for STRonGR
------------------------------------

Every single pipeline must come with a minimal installation environment. It contains the conda recipe for each single of them. You can now understand, that given the perspective of hosting an increasing number of pipelines, with various sources, purposes and requirements, there will never be a unique STRonGR environment.

However, if you want a good start, please consider creating a STRonGR environment with the following:

.. code-block:: yaml

  name: STRonGR
  channels:
    - bioconda
    - conda-forge
    - defaults
  dependencies:
    - pytest ==5.4.3
    - python ==3.8.2
    - datrie ==0.8.2
    - git ==2.27.0
    - jinja2 ==2.11.2
    - pygraphviz ==1.5
    - flask ==1.1.2
    - pip ==20.1.1
    - pandas ==1.0.4
    - zlib ==1.2.11
    - openssl ==1.1.1g
    - networkx ==2.4
    - snakemake ==5.19.2
    - sphinx  ==3.1.1
    - sphinx_rtd_theme ==0.4.3


Save this file under YAML format, then use:


.. code-block:: sh

  conda env create --file /path/to/your/env.yaml

If you already possess one or multiple of these pre-requisites, then you do not need to build this whole environment.

If you intend to use only one STRonGR pipeline, then consider using the dedicated environment of the pipeline.

Clone and test this repository
------------------------------

To finish with, clone the `STRonGR Git <https://github.com/gustaveroussy/STRonGR.git>`_:

.. code-block:: sh
  :linenos:

  # Clone git repository
  git clone https://github.com/gustaveroussy/STRonGR.git

  # Test documentation
  cd STRonGR/test           # Go to repository
  conda activate STRonGR    # Activate conda env
  make all-unit-tests       # Test your installation