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chanzuckerberg / cellxgene

An interactive explorer for single-cell transcriptomics data
https://chanzuckerberg.github.io/cellxgene/
MIT License
626 stars 116 forks source link

Clarify installation recommendation with Conda #1803

Open ambrosejcarr opened 4 years ago

ambrosejcarr commented 4 years ago

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 commented 3 years ago

@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).

signechambers1 commented 3 years ago

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

MaximilianLombardo commented 3 years ago

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.

signechambers1 commented 2 years ago

@MaximilianLombardo can this ticket be closed now?

smoe commented 3 months ago

The installation of CELLxGENE is tricky - if it is not working out of the box this means :) On https://github.com/chanzuckerberg/cellxgene/issues/2677 I give some feedback on what may happen, and also mention a bit of a confusion on using pip vs pipx. Every additional bit of information helps.