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maximilianh / cellBrowser

main repo: https://github.com/ucscGenomeBrowser/cellBrowser/ - Python pipeline and Javascript scatter plot library for single-cell datasets, http://cellbrowser.rtfd.org
https://github.com/ucscGenomeBrowser/cellBrowser/
GNU General Public License v3.0
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expression coloring slow ... hosting advice? #198

Closed Gibbsdavidl closed 3 years ago

Gibbsdavidl commented 3 years ago

Hi there,

In a larger data set of about 91K cells, it takes about a minute to color the cells after selecting a gene (say 'IL6'). I'm using google firebase to host it and I'm using the dev version.

I notice that in https://cells.ucsc.edu/, with the Autism data set, the coloring is way way faster.

Any advice? How is that done?

Thanks! -dave

maximilianh commented 3 years ago

Hmm. Can you share the dataset URL or the dataset input files ? (Not the html output files). I can debug it and see what the problem is. I suspect it’s fire base related and it’s unable to do byte range requests.

On Tue 8 Dec 2020 at 20:32, David L Gibbs notifications@github.com wrote:

Hi there,

In a larger data set of about 91K cells, it takes about a minute to color the cells after selecting a gene (say 'IL6'). I'm using google firebase to host it and I'm using the dev version.

I notice that in https://cells.ucsc.edu/, with the Autism data set, the coloring is way way faster.

Any advice? How is that done?

Thanks! -dave

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Gibbsdavidl commented 3 years ago

Yep. It's a firebase problem. I just tried hosting it right out of a google bucket.. and it's a million times faster.

Here's the instructions for future people: https://cloud.google.com/storage/docs/hosting-static-website

maximilianh commented 3 years ago

We can host the dataset for you at UCSC, for free. If you’re interested in that. Thanks for the URL!

On Tue 8 Dec 2020 at 21:29, David L Gibbs notifications@github.com wrote:

Yep. It's a firebase problem. I just tried hosting it right out of a google bucket.. and it's a million times faster.

Here's the instructions for future people: https://cloud.google.com/storage/docs/hosting-static-website

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