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
4. /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

NORMAL PIPELINE EXECUTION CODE	BITIA EXECUTION CODE

2. Using samtools to view a fastq file with different file name as provided in url

NORMAL PIPELINE EXECUTION CODE	BITIA EXECUTION CODE

3. Using Fastqc to do Quality check on a fastq file with same file name as provided

NORMAL PIPELINE EXECUTION CODE	BITIA EXECUTION CODE