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README.qmd
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---
format: gfm
---
<!-- README.md is generated from README.qmd. Please edit that file -->
# CCBR Tools
Utilities for CCBR Bioinformatics Software
[](https://github.com/CCBR/Tools/actions/workflows/build-python.yml)
[](https://github.com/CCBR/Tools/actions/workflows/docs-quartodoc.yml)
[](https://codecov.io/gh/CCBR/Tools)
[](https://doi.org/10.5281/zenodo.13377166)
## Installation
On biowulf you can access the latest release of `ccbr_tools` by loading the ccbrpipeliner module:
```sh
module load ccbrpipeliner
```
Outside of biowulf, you can install the package with pip:
```sh
pip install git+https://github.com/CCBR/Tools
```
Or specify a specific tagged version or branch:
```sh
pip install git+https://github.com/CCBR/Tools@v0.1.0
```
## Usage
### CLI
```sh
ccbr_tools --help
```
```{python}
#| echo: false
!ccbr_tools --help
```
### Python
```{python}
import ccbr_tools.pkg_util
print(ccbr_tools.pkg_util.get_version())
```
## CLI Utilities
Command-line utilities in CCBR Tools.
```{python}
#| echo: false
#| output: asis
print("\n".join([f" - `{cmd}`" for cmd in ccbr_tools.pkg_util.get_project_scripts()]))
```
Run a command with `--help` to learn how to use it.
## External Scripts
Additional standalone scripts for various common tasks in [scripts/](scripts/) are added to the path when this package is installed.
They are less robust than the CLI Utilities included in the package and do not have any unit tests.
```{python}
#| echo: false
#| output: asis
from ccbr_tools.pkg_util import get_pyproject_toml
from pathlib import Path
print('\n'.join([f" - `{Path(script).name}`" for script in get_pyproject_toml()['tool']['setuptools']['script-files']]))
```
## Citation
Please cite this software if you use it in a publication:
```{python}
#| echo: false
#| output: asis
!ccbr_tools cite -f apalike | sed -E 's/^/> /g'
```
### Bibtex entry
```{python}
#| echo: false
!ccbr_tools cite -f bibtex
```