index.md

# BioInformatics Tool for Infrastructure Automation(BiTIA)



<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 **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.

[see some examples]: examples

```{toctree}
:hidden: true

getting_started/Installation
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:: 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.


  ```{eval-rst}
  .. 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
  ```
</details>

<details>
<summary><b>GETTING_STARTED</b></summary>

- To Learn about Bio-Informatics pipelines ofs RNA-seq analysis refer 
[Bioinformatics pipelines](https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/)

- To Understand working with BiTIA refer [Working with BiTIA CLI](getting_started/Working.md)

</details>




<!-- 
```{eval-rst}
.. automodule:: bitia
``` -->