This repository is a collection of helper tools and useful scipts for internal and
external use. The CUBI tools are implemented with minimal dependencies outside of the
Python standard library (Python v3.11). Currently, the only non-standard packages are
toml
and semver
, which must be available to execute any CUBI tool.
- Clone the repository and change into the repository root directory.
- Create the Conda environment specified in
envs/conda/cubi-tools-dev.yaml
:conda env create -f envs/conda/cubi-tools-dev.yaml
- Activate the environment:
conda activate cubi-tools-dev
- Install the CUBI tools:
pip install --editable .
- Clone the repository and change into the repository root directory.
- Create the Conda environment specified in
envs/conda/cubi-tools.yaml
:conda env create -f envs/conda/cubi-tools.yaml
- Activate the environment:
conda activate cubi-tools
- Install the CUBI tools:
pip install .
ct-git
: automate initializing, cloning and normalizing git repositories -> ct-git docsct-upd-md
: creates or updates metadata files in a CUBI repository -> ct-upd-md docsct-upd-wf
: creates or updates the CUBI (Snakemake) workflow template in a CUBI repository -> ct-upd-wf docsct-hpc
: collect infos about the cluster/machine configuration (ONLY WORKS WITH PBS Pro) -> ct-hpc docs
This example specifies the metadata and workflow template versions explicitly (latest versions at the time of writing).
$ ct-git --init workflow-smk-foobar --init-preset all
$ ct-upd-md --target-dir workflow-smk-foobar/ --git-branch v1.6.1
$ ct-upd-wf --workflow-target workflow-smk-foobar/ --branch v1.4.0
If not indicated otherwise above, please follow these instructions to cite this repository in your own work.