Don't use bioconda environments in docker image

[maxulysse]

cf nf-core/cookiecutter#29

See nf-core/chipseq#10 (comment) by @tiagochst:

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• Changed RUN conda env create -f /environment.yml to RUN conda env update -n root --file environment.yml because of the source below:

  • If you are using the Conda package manager, avoid creating a Conda environment. Instead, update the root environment with whatever dependencies you want to install.

    As an example to the above warning, it would be best practice to run this: RUN conda env update -n root --file environment.yml and avoid this: RUN conda env create -f environment.yml

https://docs.datascience.com/en/master/appendix-1/dockerfile-basics-and-best-practices-1.html