index.md

BioInformatics Tool for Infrastructure Automation(BiTIA)

:target: https://pypi.python.org/pypi/bitia

:target: https://www.python.org

Welcomme to BiTIA Documentation!

BiTIA is a tool that simplifies the infrastructure required to run complex bioinformatics pipelines. BiTIA plays well with the existing pipeline solution such as snakemake.

BiTIA has two components: bitia-cli and bitia-runner. BiTIA CLI is on the clientside and allows clients to submit tasks to the bitia server. BiTIA runner is on the serverside and operates the given tasks to produce results.

bitia-cli

Most users only need the bitia-cli tool to submit tasks. BiTIA CLI creates a zip file of the user input(pipeline) containing a unique hash and ships it to the server.

:hidden: true

getting_started/Installation
getting_started/Working

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If you want to learn how to use BiTIA and installation, check out the following resources:

REQUIREMENTS

• Python 3.8+

INSTALLATION & CONFIGURATION

To Install BiTIA using pip, run this command:

.. tabs::

  .. group-tab:: Unix

            ..  code-block:: bash
  
                $ python3 -m pip install bitia


  .. group-tab:: Windows
         
            ..  code-block:: bash
         
                $ python3 -m pip install bitia

Configuration

TODO: Order of searching configuration file.

.. tabs::

  .. group-tab:: Unix

            ..  code-block:: bash

                1. ./bitia.toml  
                2. ~/.bitia.toml  
                3. $HOME/.config/bitia.toml  
                4. /etc/bitia.toml

  .. group-tab:: Windows
         
            ..  code-block:: bash

                   1. bitia.toml
                   2. %APPDATA%\bitia.toml
                   3. %PROGRAMDATA%\bitia.toml

GETTING_STARTED

• To Learn about Bio-Informatics pipelines ofs RNA-seq analysis refer Bioinformatics pipelines

• To Understand working with BiTIA refer Working with BiTIA CLI