How to rebuild all resources?

[cthoyt]

If I want to run this locally, how do I build all of the resources? It looks like there are a ton of hard-coded file paths thoughout the code. Perhaps consider using pystow to make portable filepaths.

Specific follow-up issues:

• Where do raw data files for Cell Ontology and Cellosaurus come from #7

[mjeensung]

Hi!

Thank you very much for your interest in our work.

Thank you for letting us know about the hard-coded file paths. We went through our codes and removed the hard-coded file paths from them as much as possible. We didn't use pystow this time, but we'll consider using it the next time. Please let us know if you come across any other code that still has hard-coded file paths

By the way, if you want to run the BERN2 server locally, just follow the installation manual (https://github.com/dmis-lab/BERN2#installing-bern2). Please let us know if you find anything unclear in the manual.

[dhimmel]

We went through our codes and removed the hard-coded file paths from them as much as possible

I think this is referring to the following commits:

• 8bfdeea
• 0890465

[mjeensung]

Hi @cthoyt

Have you been able to run BERN2 locally?
I'd be happy to assist you if you have any problems running it locally.