# WORKING WITH BiTIA
To List available commands and options in bitia, execute `bitia --help`
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<span data-ty="input">python -m bitia --help </span>
<span data-ty>Usage: python -m bitia [OPTIONS] COMMAND [ARGS]...
<b>Callback</b>
<b><i>Options</i></b> <br><br>
<b>--verbose</b> [debug|info|warning] [default: VerbosityLevel.warning]<br>
<b>--plain</b> --no-plain [default: no-plain] <br>
<b>--server</b> TEXT [default: None] <br>
<b>--install-completion</b> Install completion for the current shell. <br>
<b>--show-completion</b> Show completion for the current shell, to copy it or customize the installation. <br>
<b>--help </b> Show this message and exit. <br>
<b><i>Commands</i></b> <br><br>
<b>checksum</b> value that represents the number of bits in a transmission message<br>
<b>create-container</b> Create container for the pipeline. The container starts running immediately on the server. Use command `logs` to stream the output. <br>
<b>list-container</b> List the remote server associated with the pipeline. <br>
<b>logs</b> Stream logs for the most recent run of a given pipeline. <br>
<b>run</b> Run a pipeline <br>
<b>submit</b> Submit your pipelin (url, directory, zip_file). <br>
<b>version</b> version information <br>
</span>
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The three commands that are the core of BiTIA's functionality are:
- run
- submit
- logs
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## Bitia run
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<span data-ty="input"><b>python -m bitia run --help</span>
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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.
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### 1. Running commands
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<span data-ty="input">bitia run "samtools convert <foo.fa|http://y.com/foo.fa>"</span>
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The above code will:
- Checks for the input file `foo.fa` in the current working directory
- Download the input file from the given link `http://example.com/foo.fa` and name it `foo.fa`
- Add the given command `samtools convert <foo.fa|http://example.com/foo.fa` into a pipeline file.
- Extract the current working directory with the pipeline as a zip file that contains a unique hash and send it to the server `public.bitia.link`
- The BiTIA runner in the server will execute the pipeline by:
- Installing the given command `samtools`
- Downloading the given input file from the link `http://example.com/foo.fa` and name it `foo.fa`
- Executing the command `samtools convert foo.fa`
- Display the resulting output to the user console
### 2. Running Pipelines
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<span data-ty="input">bitia run pipeline.sh</span>
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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. Running Directories with multiple required files
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<span data-ty="input">bitia run work/</span>
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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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