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`cookiecutter` Data Science Template using `snakemake`, `docker`, `R` and `python`

Home Page: https://github.com/erblast/cookie_ds_demo

License: Other

Python 33.21% Dockerfile 26.99% R 20.80% Jupyter Notebook 19.01%

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cookie_ds's Issues

refactor

  • use format not + in cookiecutter.json
  • make demo ci/cd sketch
  • move copy all code into container statement to the end of dockerfile
  • correct library chunk options in Rmd files
  • hardcoded package path in snakemake lint
  • improve R shell command
  • hardcoding paths in render doc rmd
  • adjust configuration strategy
  • add docs/_site to .gitignore
  • successfull linting should return message
  • debug folder missing?
  • add snakemake --keep-incomplete for test run to README
  • git page does not link to R package documentation correctly
  • copy conda yaml isntead of using from /repo/envs
COPY envs/cookiedsdemo_conda.yml /files/envs/
RUN conda env update --file /files/envs/cookiedsdemo_conda.yml
  • mkdocs

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