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Novartis / cellxgene-gateway

Cellxgene Gateway allows you to use the Cellxgene Server provided by the Chan Zuckerberg Institute (https://github.com/chanzuckerberg/cellxgene) with multiple datasets.
Apache License 2.0
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Customizations to the UI #79

Closed tkakar closed 1 year ago

tkakar commented 1 year ago

Thank you for developing the cellxgene-gateway, it seems pretty convenient.

I'm following the docs to customize the UI by changing the styles/html files. When I run the run.sh.example I can see my changes. But dockerizing it using the provided docker file does not show changes, probably it uses the installed version of the cellxgene-gateway using RUN pip install cellxgene-gateway 'MarkupSafe<2.1'?.

I'm unable to make it work properly using the development guidelines. Executing setup.py throws error. Processing dependencies for cellxgene-gateway==0.3.10 Searching for certifi>=2017.4.17 Reading https://pypi.org/simple/certifi/ Download error on https://pypi.org/simple/certifi/: unknown url type: https -- Some packages may not be found! Couldn't find index page for 'certifi' (maybe misspelled?) Scanning index of all packages (this may take a while) Reading https://pypi.org/simple/ Download error on https://pypi.org/simple/: unknown url type: https -- Some packages may not be found! No local packages or working download links found for certifi>=2017.4.17 error: Could not find suitable distribution for Requirement.parse('certifi>=2017.4.17')

Is anyone experiencing similar issue? How can I make docker container read the changes? Or run it in the develop mode without the run.sh.example file?
Appreciate your help.

alokito commented 1 year ago

Hi @tkakar ! You are correct that pip install cellxgene-gateway will use the published version of cellxgene-gateway from PyPI, not the one in the local folder. I would actually recommend customizing this version within the dockerfile rather than checking out the repo and customizing it here. You can see an example of this here: https://github.com/Novartis/cellxgene-gateway/tree/79_add_docker_example/examples/customized_docker_image hope it helps!

tkakar commented 1 year ago

@alokito Thank you, this worked perfectly!

alokito commented 1 year ago

This is merged into master, please open a new ticket if there are any remaining issues.