Pre-release
This release is a pre-release and may not be stable for production use.
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
./bitia.toml~/.bitia.toml$HOME/.config/bitia.toml/etc/bitia.toml
Windows
bitia.toml%APPDATA%\bitia.toml%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
- 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>"
- 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>"
1 maintainer
Metadata
1 maintainer
Release files for bitia 0.2.0.dev1667816528
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Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
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| bitia-0.2.0.dev1667816528-py3-none-any.whl | Python 3 | none | any | Details |
Release files / bitia-0.2.0.dev1667816528-py3-none-any.whl
| Download URL | bitia-0.2.0.dev1667816528-py3-none-any.whl |
|---|---|
| Size | 24.5 kB |
| Tags | Python 3 |
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