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bioconda / bioconda-recipes

Conda recipes for the bioconda channel.
https://bioconda.github.io
MIT License
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How to include dependencies of Python and R packages not in conda? #37119

Open lijinbio opened 1 year ago

lijinbio commented 1 year ago

Hi all,

I want to create a receipt by depending on Python and R packages that are not in conda. Say, https://pypi.org/project/dropkick/ https://github.com/chris-mcginnis-ucsf/DoubletFinder

They are not in conda yet, and they can be installed locally by pip and remotes::install_github(). But how could I specify them as dependencies in the receipt's meta.yaml? Thanks.

mptrsen commented 1 year ago

Create recipes for the dependencies first to make them available in conda.

lijinbio commented 1 year ago

Hi @mptrsen, thanks for your comments. I am not a developer of those packages, and I am not so sure about correct dependences of them. May I ask if conda supports a workaround to install dependences from PyPI and GitHub directly. Thanks.

mjsteinbaugh commented 1 year ago

@lijinbio Yeah these need to be added to conda-forge or bioconda. I can take a look into creating a recipe for DoubletFinder later this week.

lijinbio commented 1 year ago

Thanks @mjsteinbaugh so much.

lijinbio commented 1 year ago

Hi @mjsteinbaugh, may I ask if you might have any update on this? Thank you so much.

mjsteinbaugh commented 1 year ago

Hi @lijinbio sorry have been super busy -- I've made a note to take a look when I have some free time

lijinbio commented 1 year ago

Hi @mjsteinbaugh, sure thing. Thank you so much for all your help.