Metadata-Version: 2.1
Name: bitia
Version: 0.2.0.dev1667205459
Summary: BioInformatics Tool for Infrastructure Automation (BiTIA) CLI utility.
Author: Dilawar Singh
Author-email: dilawar@subcom.tech
Requires-Python: >=3.8,<4.0
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Requires-Dist: pyparsing (>=3.0.9,<4.0.0)
Requires-Dist: requests (>=2.28.1,<3.0.0)
Requires-Dist: rich (>=12.5.1,<13.0.0)
Requires-Dist: typer (>=0.6.1,<0.7.0)
Requires-Dist: validators (>=0.20.0,<0.21.0)
Description-Content-Type: text/markdown



# BioInformatics Tool for Infrastructure Automation (BiTIA) CLI utility

This is the cli utility of the BiTIA project. The other component is
`bitia-runner`. Most users only need the cli client `bitia` to submit jobs.
Install it using `pip`.

```
python -m pip install bitia --user
python -m bitia --help
```

## Configuration

TODO: Order of searching configuration file.

### Unix like systems

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


### Windows

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

## BiTIA runner

If you are self-hosting the BiTIA server, you need `bitia-runner` as well. See
the documents of `bitia-runner` for more details. TODO.


## EXAMPLES

1. Using samtools to view a fastq file

<div style="display: grid;grid-template-columns: 1fr 1fr;grid-gap: 20px;flex-direction:row;">


<div style="padding-left: 40px;">

<h3>NORMAL PIPELINE EXECUTION CODE</h3>
<img src="./docs/source/img/readme_example_1.gif"  />
</div>


<div >

<h3>BITIA EXECUTION CODE</h3>
<img src="./docs/source/img/readme_example_1_bitia.gif"  />

</div>
</div>
