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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 
<!-- 
<div class="tab">
  <button class="tablinks" onclick="openCity(event, 'London')">Ubuntu</button>
  <button class="tablinks" onclick="openCity(event, 'Paris')">Arch</button>
  <button class="tablinks" onclick="openCity(event, 'Tokyo')">BiTIA</button>
</div>


<div id="London" class="tabcontent">
  <div id="termynal" data-termynal>
    <span data-ty="input">sudo apt get install wget samtools</span>
    <span data-ty="input">wget https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq</span>
    <span data-ty="input">samtools convert 1_control_18S_2019_minq7%20-%20Copy.fastq</span>
</div>  
</div>

<div id="Paris" class="tabcontent">
  <div id="termynal1" data-termynal>
    <span data-ty="input">pacman -S wget samtools</span>
    <span data-ty="input">wget https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq</span>
    <span data-ty="input">samtools convert 1_control_18S_2019_minq7%20-%20Copy.fastq</span>
</div>  
</div>

<div id="Tokyo" class="tabcontent">
  <div id="termynal2" data-termynal>
    <span data-ty="input">bitia run "samtools convert &lt;sample.fastq|https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq&gt;"</span>
</div>
</div>



 -->

<div class="tab">
  <button class="tablinks" onmouseover="openCity(event, 'Ubuntu')">Ubuntu</button>
  <button class="tablinks" onmouseover="openCity(event, 'Pacman')">Pacman</button>
  <button class="tablinks" onmouseover="openCity(event, 'BiTIA')">BiTIA</button>
</div>

<div id="Ubuntu" style="display: block;" class="tabcontent">
  <div id="termynal" data-termynal>
    <span data-ty="input">sudo apt get install wget samtools</span>
    <span data-ty="input">wget https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq</span>
    <span data-ty="input">samtools convert 1_control_18S_2019_minq7%20-%20Copy.fastq</span>
</div>
</div>

<div id="Pacman" style="display: none;"class="tabcontent">
  <div id="termynal1" data-termynal>
    <span data-ty="input">pacman -S wget samtools</span>
    <span data-ty="input">wget https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq</span>
    <span data-ty="input">samtools convert 1_control_18S_2019_minq7%20-%20Copy.fastq</span>
    </div> 
</div>

<div id="BiTIA" style="display: none;" class="tabcontent">
  <div id="termynal2" data-termynal>
    <span data-ty="input">bitia run "samtools convert &lt;https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq&gt;"</span>
</div>
</div>

<div class="clearfix"></div>


2. Using samtools to view a fastq file with different file name as provided in url
   
<div class="tab">
  <button class="tablinks" onmouseover="openCity(event, 'UBUNTU')">Ubuntu</button>
  <button class="tablinks" onmouseover="openCity(event, 'PACMAN')">Pacman</button>
  <button class="tablinks" onmouseover="openCity(event, 'BITIA')">BiTIA</button>
</div>

<div id="UBUNTU" style="display: block;" class="tabcontent">
  <div id="termynal3" data-termynal>
    <span data-ty="input">sudo apt get install wget samtools</span>
    <span data-ty="input">wget sample.fastq https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq</span>
    <span data-ty="input">samtools convert sample.fastq</span>
</div>
</div>

<div id="PACMAN"  style="display: none;"class="tabcontent">
  <div id="termynal4" data-termynal>
    <span data-ty="input">pacman -S wget samtools</span>
    <span data-ty="input">wget sample.fastq https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq</span>
    <span data-ty="input">samtools convert sample.fastq</span>
    </div> 
</div>

<div id="BITIA" style="display: none;" class="tabcontent">
  <div id="termynal5" data-termynal>
    <span data-ty="input">bitia run "samtools convert &lt;sample.fastq|https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq&gt;"</span>
</div>
</div>

<div class="clearfix"></div>


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