bitia 0.2.0.dev1667901904

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

Ubuntu Pacman BiTIA

sudo apt get install wget samtools wget https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq samtools convert 1_control_18S_2019_minq7%20-%20Copy.fastq

pacman -S wget samtools wget https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq samtools convert 1_control_18S_2019_minq7%20-%20Copy.fastq

bitia run "samtools convert <https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq>"

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

Ubuntu Pacman BiTIA

sudo apt get install wget samtools wget sample.fastq https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq samtools convert sample.fastq

pacman -S wget samtools wget sample.fastq https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq samtools convert sample.fastq

bitia run "samtools convert <sample.fastq|https://zenodo.org/record/3736457/files/1_control_18S_2019_minq7%20-%20Copy.fastq>"

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