Working.md

# Working with BiTIA CLI
BiTIA has three commands to work on it:
- run
- submit
- logs

### Bitia run can be employed in following ways:

#### 1. Running commands

```bash
$ bitia run "samtools convert foo.fa#http://example.com/foo.fa"
```
The above code will 
- Add the given command `samtools run foo.fa#http://example.com/foo.fa` into a pipeline file.
- Extract the current working directory with the pipeline as zip file with a unique hash and sent to the server `public.bitia.link`
- The BiTIA runner in the server will execute the pipeline 
    - Installs the given command  `samtools`
    - Download the given input file form the link  `http://example.com/foo.fa` and name it as `foo.fa`
    - execute the command `samtools convert foo.fa` 
- Displays the resulting output to the user console

#### 2. Running Pipelines

```bash
$ bitia run pipeline.sh
```
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 zip file with a unique hash and sent to the server `public.bitia.link`
- The BiTIA runner in the server will execute the pipeline 
    - Installs the given commands `fastqc`, `trim_galore`,`hisat2` .
    - executes the commands given in the pipeline
- Displays the resulting output to the user console