Utilities for CCBR Bioinformatics Software

build docs codecov DOI

Installation

On biowulf you can access the latest release of ccbr_tools by loading the ccbrpipeliner module:

module load ccbrpipeliner

Outside of biowulf, you can install the package with pip:

pip install git+https://github.com/CCBR/Tools

Or specify any tagged version or branch:

pip install git+https://github.com/CCBR/Tools@v0.2.4

Basic usage

CLI

ccbr_tools --help
Usage: ccbr_tools [OPTIONS] COMMAND [ARGS]...

  Utilities for CCBR Bioinformatics Software

  For more options, run: ccbr_tools [command] --help

  https://ccbr.github.io/Tools/

Options:
  -v, --version  Show the version and exit.
  -h, --help     Show this message and exit.

Commands:
  send-email  Send an email (works on biowulf)
  quarto-add  Add a quarto extension
  install     Install a specific version of a CCBR software package,...
  cite        Print the citation in the desired format
  version     Print the version of ccbr_tools

All installed tools:
  ccbr-hooks
  ccbr_tools
  gb2gtf
  get_hpcname
  hf
  intersect
  jobby
  jobinfo
  module_list
  peek
  spooker

Pre-commit hooks

Add the hooks to your .pre-commit-config.yaml file:

 - repo: https://github.com/CCBR/Tools
   rev: v0.5.0
   hooks:
     - id: detect-absolute-paths

View the reference guide on pre-commit hooks for more information.

Python

Code 
import ccbr_tools.shell
print(ccbr_tools.shell.shell_run('echo "Hello, world!"'))
Hello, world!
Code 
import ccbr_tools.versions
version = ccbr_tools.versions.match_semver('0.2.3')
version.groupdict()
{'major': '0',
 'minor': '2',
 'patch': '3',
 'prerelease': None,
 'buildmetadata': None}

View the API reference for more information.

Help & Contributing

Come across a bug? Open an issue and include a minimal reproducible example.

Have a question? Ask it in discussions.

Want to contribute to this project? Check out the contributing guidelines.