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updated documentation

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# Getting Started # Getting Started
BiTIA CLI is the Command Interface tool helpful in getting user inputs with commands and required files, directories etc.
## Installation This submits jobs to the server, which contains bitia-runner that works on the job and produce results
BiTIA is available on PyPi.
To get started with using BiTIA, you should [install Python] and make sure [python-pip] is installed with it on your system. **To work with BiTIA, we need to install bitia-cli and submit jobs to the server**
## Installing bitia
Installing bitia is very simple, you only need to have [python-pip] installed in your system
[install Python]: https://realpython.com/installing-python/ BiTIA CLI is available on [PyPi] as [BiTIA].
[python-pip]: https://pypi.org/project/pip/ #### Ensure you have a working pip
### Ensure you have a working pip
As a first step, you should check that you have a working Python with pip As a first step, you should check that you have a working Python with pip
installed. This can be done by running the following commands and making installed. This can be done by running the following commands and making
...@@ -26,7 +27,12 @@ If that worked, congratulations! You have a working pip in your environment. ...@@ -26,7 +27,12 @@ If that worked, congratulations! You have a working pip in your environment.
To Install **BiTIA** using pip: To Install **BiTIA** using pip:
```bash ```
$ python3 -m pip install bitia $ python3 -m pip install bitia
``` ```
[BiTIA]: https://pypi.org/project/bitia/
[Pypi]: https://pypi.org/
[install Python]: https://realpython.com/installing-python/
[python-pip]: https://pypi.org/project/pip/
\ No newline at end of file
## BioInformatics Tool for Infrastructure Automation (BiTIA) ## BioInformatics Tool for Infrastructure Automation (BiTIA)
```{image} https://img.shields.io/pypi/v/bitia.svg ```{image} https://img.shields.io/pypi/v/bitia.svg
:target: https://pypi.python.org/pypi/bitia :target: https://pypi.python.org/pypi/bitia
``` ```
```{image} https://img.shields.io/pypi/pyversions/bitia.svg ```{image} https://img.shields.io/pypi/pyversions/bitia.svg
:target: https://www.python.org :target: https://www.python.org
``` ```
BiTIA is a tool that simplifies the infrastructure required to run complex bioinformatics pipelines. BiTIA plays well with the existing pipeline solution such as snakement.
BiTIA has two components: bitia-cli and bitia-runner.
BiTIA makes it easy to orchestrate the infrastructure required to run - **bitia-cli**
complex bioinformatics pipelines. BiTIA plays well with existing pipeline Creates a zip file of the user input(pipeline) containing a unique hash and ships it to the server.
solution such as snakemake. [See some examples] - **bitia-runner**
Runs following works in the server
- Creates a docker container with the user input
- Runs the pipeline
- Sends log to the user
- Sends link of results(artifacts) to the user
- Interacts with common cache for reading data/reference files
[see some examples]: examples [see some examples]: examples
...@@ -18,7 +26,6 @@ solution such as snakemake. [See some examples] ...@@ -18,7 +26,6 @@ solution such as snakemake. [See some examples]
```{toctree} ```{toctree}
:caption: Getting started :caption: Getting started
:hidden: true :hidden: true
:maxdepth: 1
:name: getting_started :name: getting_started
getting_started getting_started
...@@ -26,7 +33,7 @@ developer ...@@ -26,7 +33,7 @@ developer
``` ```
If you want to learn how to use BiTIA, check out the following resources: If you want to learn how to use BiTIA and installation, check out the following resources:
- [Getting Started](getting_started.md) - [Getting Started](getting_started.md)
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