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# Getting Started
BiTIA CLI is the Command Interface tool helpful in getting user inputs with commands and required files, directories etc.
## Installation
BiTIA is available on PyPi.
This submits jobs to the server, which contains bitia-runner that works on the job and produce results
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/
[python-pip]: https://pypi.org/project/pip/
### Ensure you have a working pip
BiTIA CLI is available on [PyPi] as [BiTIA].
#### Ensure you have a working 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
......@@ -26,7 +27,12 @@ If that worked, congratulations! You have a working pip in your environment.
To Install **BiTIA** using pip:
```bash
```
$ 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)
```{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
```
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 makes it easy to orchestrate the infrastructure required to run
complex bioinformatics pipelines. BiTIA plays well with existing pipeline
solution such as snakemake. [See some examples]
BiTIA has two components: bitia-cli and bitia-runner.
- **bitia-cli**
Creates a zip file of the user input(pipeline) containing a unique hash and ships it to the server.
- **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
......@@ -18,7 +26,6 @@ solution such as snakemake. [See some examples]
```{toctree}
:caption: Getting started
:hidden: true
:maxdepth: 1
:name: getting_started
getting_started
......@@ -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)
......
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