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KarchinLab / open-cravat

A modular annotation tool for genomic variants
MIT License
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Connection to store.opencravat.org timed out #145

Closed kkmarkel closed 1 year ago

kkmarkel commented 1 year ago

Hi there! Every time I run oc module install-base it stops promptly with an error:

ERROR
HTTPSConnectionPool(host='store.opencravat.org', port=443): Max retries exceeded with url: /modules/casecontrol/1.2.0/casecontrol.yml (Caused by ConnectTimeoutError(<urllib3.connection.HTTPSConnection object at 0x7f5ecf741a90>, 'Connection to store.opencravat.org timed out. (connect timeout=3)'))
Repeat command with --debug for more details

Is it caused on my side because of my connection to the server? Has anybody encountered that as well?

Maybe there is a way to increase connect timeout?

PS: I run open-cravat not under sudo, installed it using pip in a venv.

kmoad commented 1 year ago

Probably is a network timeout. If you run again with --debug it should show exactly which request, and we can increase the timeout.

You could also try one of the AWS mirrors. Instructions here https://open-cravat.readthedocs.io/en/latest/AWS-OpenData.html

kkmarkel commented 1 year ago

It seems this problem appeared to be only temporary and the downloads run normally now. I suspect it could be caused by installing many annotators at once :sweat_smile: Thanks a lot for the reply and your advice about the AWS mirrors!