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yyoshiaki / VIRTUS2

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
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createindex #14

Closed inagaki-s closed 1 year ago

inagaki-s commented 1 year ago

" cwltool createindex.cwl https://raw.githubusercontent.com/yyoshiaki/VIRTUS2/master/workflow/createindex.job.yaml" I tried to run createindex in the workflow directory, but I get the following error. What could be the cause?

ERROR Tool definition failed validation: Error fetching https://raw.githubusercontent.com/yyoshiaki/VIRTUS2/master/workflow/createindex.job.yaml: HTTPSConnectionPool(host='raw.githubusercontent.com', port=443): Max retries exceeded with url: /yyoshiaki/VIRTUS2/master/workflow/createindex.job.yaml (Caused by NewConnectionError('<urllib3.connection.VerifiedHTTPSConnection object at 0x7f0eca94e6a0>: Failed to establish a new connection: [Errno -2] Name or service not known'))

yyoshiaki commented 1 year ago

This looks like a network issue in downloading the input yaml file. you can manually download the YAML file (https://raw.githubusercontent.com/yyoshiaki/VIRTUS2/master/workflow/createindex.job.yaml) and specify it instead of the URL, such as cwltool createindex.cwl createindex.job.yaml.

inagaki-s commented 1 year ago

I was able to solve the problem. Thank you very much.