# BioInformatics Tool for Infrastructure Automation(BiTIA) ```{image} img/bitia.png :align: center :height: 100 :width: 100 ``` <p align="center"> ```{image} https://img.shields.io/pypi/v/bitia.svg :target: https://pypi.python.org/pypi/bitia ``` ```{image} https://img.shields.io/pypi/pyversions/bitia.svg :target: https://www.python.org ``` </p> 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 **bitita-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. [see some examples]: examples ```{toctree} :hidden: true getting_started/Installation getting_started/bioinformatics getting_started/Working ``` *** If you want to learn how to use BiTIA and installation, check out the following resources: <details > <summary><b>REQUIREMENTS</b></summary> > - Python 3.8+ </details> <details> <summary><b>INSTALLATION & CONFIGURATION</b></summary> To Install BiTIA using pip, run this command: ```{eval-rst} .. tabs:: .. group-tab:: Linux .. code-block:: bash $ python3 -m pip install bitia .. group-tab:: MacOS .. 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. ```{eval-rst} .. tabs:: .. group-tab:: Linux .. code-block:: bash 1. ./bitia.toml 2. ~/.bitia.toml 3. $HOME/.config/bitia.toml 4. /etc/bitia.toml .. group-tab:: MacOS .. 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 ``` </details> <details> <summary><b>GETTING_STARTED</b></summary> To Learn about Bio-Informatics pipelines and RNA-seq analysis refer [Bio-Informatics pipelines](getting_started/bioinformatics.md) </details> <!-- ```{eval-rst} .. automodule:: bitia ``` -->