CUBI Toolkit

Tooling for connecting GitLab, pipelines, and SODAR at CUBI.

• Documentation

Getting Started

Clone CUBI-TK, create a conda environment and install using pip or uv.

Checkout the repository and create a conda environment:

git clone [email protected]:bihealth/cubi-tk.git
conda env create -n cubi-tk -f environment.yaml
conda activate cubi-tk
cd cubi-tk

To update an existing environment use:

conda activate cubi-tk
conda env update -f environment.yaml --prune

Install the package using pip:

$ pip install -e .

Or using uv:

# if not using conda: `uv python install 3.12`
uv python pin 3.12
uv sync
# For full development install use:
# uv sync --all-extras --all-groups --all-packages
uv pip install -e .

Building the Manual

uv sync --all-extras --group docs
cd docs_manual
uv run make clean html
xdg-open _build/html/index.html

Argument Completion

cat >>~/.bashrc <<"EOF"
eval "$(register-python-argcomplete cubi-tk)"
EOF