bitia 0.2.0.dev1670837010

BioInformatics Tool for Infrastructure Automation (BiTIA) CLI utility.

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