CUBI Toolkit

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

• Documentation

Getting Started

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

$ git clone [email protected]:bihealth/cubi-tk.git
$ conda env create -n cubi-tk -f environment.yaml
$ conda activate cubi-tk
$ cd cubi-tk
$ uv python pin 3.12
$ uv sync
$ uv pip install -e .
# or, if you need snappy kickoff:
#$ GIT_LFS_SKIP_SMUDGE=1 uv pip install -e '.[snappy]'

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