Skip to content

core-unit-bioinformatics/cubi-tools

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

CUBI tools

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.

Installation

For (CUBI) developers

  1. Clone the repository and change into the repository root directory.
  2. Create the Conda environment specified in envs/conda/cubi-tools-dev.yaml:
    • conda env create -f envs/conda/cubi-tools-dev.yaml
  3. Activate the environment:
    • conda activate cubi-tools-dev
  4. Install the CUBI tools:
    • pip install --editable .

For users

  1. Clone the repository and change into the repository root directory.
  2. Create the Conda environment specified in envs/conda/cubi-tools.yaml:
    • conda env create -f envs/conda/cubi-tools.yaml
  3. Activate the environment:
    • conda activate cubi-tools
  4. Install the CUBI tools:
    • pip install .

CLI tools available after installation

  • ct-git: automate initializing, cloning and normalizing git repositories -> ct-git docs
  • ct-upd-md: creates or updates metadata files in a CUBI repository -> ct-upd-md docs
  • ct-upd-wf: creates or updates the CUBI (Snakemake) workflow template in a CUBI repository -> ct-upd-wf docs
  • ct-hpc: collect infos about the cluster/machine configuration (ONLY WORKS WITH PBS Pro) -> ct-hpc docs

Usage examples

Initializing a new Snakemake workflow repository

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

Citation

If not indicated otherwise above, please follow these instructions to cite this repository in your own work.

About

No description, website, or topics provided.

Resources

License

Stars

Watchers

Forks

Packages

No packages published

Contributors 3

  •  
  •  
  •  

Languages