README.md

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# 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 with same name as provided in url 
 
NORMAL PIPELINE EXECUTION CODE         |  BITIA EXECUTION CODE
:-------------------------:|:-------------------------:
![](./docs/source/img/readme_example_1.gif)  |![](./docs/source/img/readme_example_1_bitia.gif)



2. Using samtools to view a fastq file with different file name as provided in url

NORMAL PIPELINE EXECUTION CODE         |  BITIA EXECUTION CODE
:-------------------------:|:-------------------------:
![](./docs/source/img/readme_example_2.gif)  |![](./docs/source/img/readme_example_2_bitia.gif)

3. Using Fastqc to do Quality check on a fastq file with same file name as provided

NORMAL PIPELINE EXECUTION CODE         |  BITIA EXECUTION CODE
:-------------------------:|:-------------------------:
![](./docs/source/img/readme_example_3.gif)  |![](./docs/source/img/readme_example_3_bitia.gif)