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Executes the pipeline in server [public.bitia.link/api](https://public.bitia.link/api/) and displays the output in the CLI simultaneously.
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<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>
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<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
For executing any single task of bioInformatics pipeline, we can instruct Bitia using single-line commands.
syntaxes for specifying tasks:
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<b>bitia</b> <b>run</b> "command <input-link>"
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<br>
<b><input-link></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>"
````
<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>
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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. Executing Directories with multiple required files
<span data-ty="input">bitia run work</span>
<span data-ty>Using server <a style="color:blue">https://public.bitia.link/api/v1</a>
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<span data-ty="progress"></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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