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opain / GenoPred

Genotype-based Prediction (GenoPred)
https://opain.github.io/GenoPred/
GNU General Public License v3.0
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Unavailability of automatically downloaded public resources #74

Closed friedav-old closed 1 year ago

friedav-old commented 1 year ago

Hi there,

the public resources from Alkes Price's group were moved to a requester-pays Google Cloud Bucket (https://console.cloud.google.com/storage/browser/broad-alkesgroup-public-requster-pays) due to excessive data transfer costs. Therefore the respective download rules of GenoPredPipe do not work anymore.

I did not have the chance to try it yet, but is it sufficient to manually download and unpack the resources into their target directories so that the output of the corresponding snakemake rules is already existent when I start the full pipeline run?

Best, Friederike

opain commented 1 year ago

Hello Friederike,

Thank you for bringing this to my attention.

I have just uploaded a copy of the HapMap3 SNP-list to Zenodo, and pushed a commit so the pipeline automatically downloads it (https://github.com/opain/GenoPred/commit/bddef186e7465fc76ac1a562a2007819423a4844). If you git pull the repo again, it should now work for you.

To answer you question, as you suggested, manually downloading the file and unpacking it to "resources/data/hm3_snplist/w_hm3.snplist" would also work.

Let me know if you run into any other issues.

Best wishes,

Ollie

friedav-old commented 1 year ago

Hello Ollie,

Thank you for the fix, seems to be working!

Best, Friederike