Command line upload

How To MapMyCells
1

Hello all,

Wondering if there is a command line upload interface in the works, for clusters and the like that don’t have browser access.

Thanks,
Rob

2

Hi Rob @rrbutler ,

Thank you for your interest in Map My Cells. Our mapping algorithm and related documentation is available on GitHub here: https://github.com/AllenInstitute/cell_type_mapper. Let me know if that helps of if you were looking for something different. I’d love to learn more about how you’d like to use our tools.

Thanks,
Elysha
Product Manager, Allen Institute for Brain Science

3

Thanks for the link Elysha, the documentation for the recent Whole mouse brain paper doesn’t actually link to this repository.

Specifically, I was looking to upload my data straight from our cluster, as it isn’t ideal to download it to my laptop to use the webportal. I was wondering if there was a command line submission tool like an API call.

However, while our previous datasets were coming in under 2GB, the current ones are just over, making it very impractical to split the experiment into its 12 samples, download 12 sample files to my laptop, upload 12 sample files to the web portal, download 12 sample files to my laptop, upload 12 sample files to the cluster.

Is there a location where we can download the precomputed h5 and json for the 10xWholeMouseBrain(CCN20230722) dataset?