# BiTIA run 

Executes the pipeline in server [public.bitia.link/api](https://public.bitia.link/api/) and displays the output in the CLI simultaneously.

<div id="termynal" data-termynal>
    <span data-ty="input"><b>bitia run --help</b></span>
    <span data-ty>Using server <a style="color:blue">https://public.bitia.link/api/v1</a>
    <span data-ty>
Usage: python -m bitia run [OPTIONS] USER_INPUT<br>                     
                                                                      
 Run a pipeline<br>                                                       
                                                                      
 <b><i>Arguments</i></b> <br><br>
 \*    <b>user_input</b>      TEXT  [default: None] [required]<br><br>
<i><b>Options</i></b> <br><br>
<b>--rerun</b>           --no-rerun          [default: no-rerun]         
<b>--output-lines </b>                 TEXT<      
<b>--help </b>                               Show this message and exit. 
</span>
</div>


The Argument `user_input` for executing tasks  can be used in three ways:
1. [Executing single line commands](#1-executing-single-line-commands)
2. [Executing pipelines](#2-executing-pipelines)
3. [Executing directories with multiple required files](#3-executing-directories-with-multiple-required-files)  

## 1. Executing Single line Commands




&nbsp; For executing any single task of bioInformatics pipeline, we can instruct Bitia using single-line commands. 


syntaxes for specifying tasks:

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 &nbsp;<b>bitia</b>&nbsp;<b>run</b>&nbsp;"command &lt;input-link&gt;"
</div>
<br>

<b>&lt;input-link&gt;</b> can be used in two ways:

1. specify url that downloads file with same name as input

````
bitia run "fastqc <https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq>"
````

2. specify filename with url where url does'nt download file with same name as input.


````
bitia run "fastqc <sampple.fastq|https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq>"
````



## 2. Executing Pipelines

<div id="termynal1" data-termynal>
    <span data-ty="input">bitia run pipeline.sh</span>
    <span data-ty>Using server <a style="color:blue">https://public.bitia.link/api/v1</a>
    <span data-ty="progress"></span>
</div>




for `pipeline.sh`:
```bash
#!/usr/bin/env bash

fastqc *.gz

for file in *_1.fastq.gz
do
   trim_galore --cores 8 --gzip --fastqc --max_n 2 --output_dir Trimmed_Data/ --paired $file ${file%_1.fastq.gz}_2.fastq.gz
done

hisat2-build -p 8 ./Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa index
```

The above code will:
- Extract the current working directory with the `pipeline.sh` as a zip file containing a unique hash and send it to the public `server.bitia.link`
- The BiTIA runner in the server will execute the pipeline .
    - Installing the given commands `fastqc`, `trim_galore`,`hisat2`.
    - executing the commands given in the pipeline
- Displays the resulting output to the user console

## 3. Executing Directories with multiple required files


<div id="termynal2" data-termynal>
    <span data-ty="input">bitia run work</span>
    <span data-ty>Using server <a style="color:blue">https://public.bitia.link/api/v1</a>
    <span data-ty="progress"></span>
</div>


Here `work` directory has two files `main.bitia.sh` and `input_file_links.txt`

for `main.bitia.sh`:
```bash
#!/usr/bin/env bash

fastqc *.gz

for file in *_1.fastq.gz
do
   trim_galore --cores 8 --gzip --fastqc --max_n 2 --output_dir Trimmed_Data/ --paired $file ${file%_1.fastq.gz}_2.fastq.gz
done

hisat2-build -p 8 ./Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa index
```

and `input_file_links.txt`
```bash
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR200/058/SRR20076358/SRR20076358_1.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR200/058/SRR20076358/SRR20076358_2.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR200/061/SRR20076361/SRR20076361_1.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR200/061/SRR20076361/SRR20076361_2.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR200/063/SRR20076363/SRR20076363_1.fastq.gz
ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR200/063/SRR20076363/SRR20076363_2.fastq.gz
```


The above code will:
- Extract the given directory with `main.bitia.sh` as a zip file containing a unique hash and send it to the public `server.bitia.link`
- The BiTIA runner in the server will execute the pipeline by:
    - Downloading the given input files which are mentioned in `input_files.txt`.
    - Installing the given commands `fastqc`, `trim_galore`,`hisat2`.
    - Executing the commands given in the pipeline
- Displays the resulting output to the user console

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