Work around access biomart in run_scenicplus biomart

[zqzneptune]

Hello,

Our HPC nodes cannot access the internet. Is there any work around for run_scenicplus to avoid trying to get information from biomart on the fly?

Thanks!

[SeppeDeWinter]

Hi @zqzneptune

These are the steps where biomart is used:

• get_search_space
• export_to_UCSC_interact

With the last step being optional.

In order to not use biomart you will have to run the get_search_space function manually prior to running the wrapper script.
To do this see: https://scenicplus.readthedocs.io/en/development/pbmc_multiome_tutorial.html#Notes-on-the-individual-function-calls-in-the-wrapper-function. Defining the search space.

After you have run this you should be able to continue using the wrapper function (run_scenicplus) without any problem (with export_to_UCSC_file set to False).

I hope this helps.

Best,

Seppe