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Clarify installation recommendation with Conda

Open ambrosejcarr opened this issue 4 years ago • 5 comments

We currently recommend installation of cellxgene in conda using pip, which is brittle to scientists installing additional packages using conda install.

Friederike Dundar suggests that we either maintain a conda recipe such as this one so that we can update the installation instructions to include conda install, or clarify that it is risky to mix pip and conda installation commands.

ambrosejcarr avatar Aug 31 '20 12:08 ambrosejcarr

@MaximilianLombardo we should update our documentation to clarify that only cellxgene should be installed in its conda environment to avoid additional packages installed on top breaking the cellxgene installation. I don't think it's necessary to maintain a recipe since cellxgene does not need to be co-imported with other python packages to function (users can use one environment for scanpy, jupyter, etc, and a second for cellxgene).

ambrosejcarr avatar Dec 23 '20 17:12 ambrosejcarr

@MaximilianLombardo is this still worth doing? Let's incorporate it or if it's too low priority close.

signechambers1 avatar Apr 06 '21 18:04 signechambers1

Let's keep this open. I will be getting to this topic during my docs rewrite towards the beginning of this quarter. We can close once this section of the docs is updated.

MaximilianLombardo avatar Apr 07 '21 15:04 MaximilianLombardo

@MaximilianLombardo can this ticket be closed now?

signechambers1 avatar Nov 08 '21 21:11 signechambers1