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yyoshiaki / VIRTUS

A bioinformatics pipeline for viral transcriptome detection and quantification considering splicing.
https://github.com/yyoshiaki/VIRTUS/wiki
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Installation Issue #20

Closed fjmuzengyiheng closed 4 years ago

fjmuzengyiheng commented 4 years ago

Hi, I get this error when I try to create indices.

Here is my command:

 createindex.cwl https://raw.githubusercontent.com/yyoshiaki/VIRTUS/master/workflow/createindex.job.yaml

An error occurred below:

INFO /home/zengyiheng/miniconda3/bin/cwltool 3.0.20200807132242 INFO Resolved '/home/zengyiheng/biosoft/virtus/VIRTUS/bin/createindex.cwl' to 'file:///home/zengyiheng/biosoft/virtus/VIRTUS/bin/createindex.cwl' ERROR Tool definition failed validation: Error fetching https://raw.githubusercontent.com/yyoshiaki/VIRTUS/master/workflow/createindex.job.yaml: HTTPSConnectionPool(host='raw.githubusercontent.com', port=443): Max retries exceeded with url: /yyoshiaki/VIRTUS/master/workflow/createindex.job.yaml (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x7f3daa117bd0>: Failed to establish a new connection: [Errno 111] Connection refused'))

I can't figure it out. Could someone help me? Thanks a lot. Yi-Heng Zeng

yyoshiaki commented 4 years ago

Thank you for trying! It looks network error. How about executing it without https like below,

createindex.cwl /path/to/createindex.job.yaml

You can find 'createindex.job.yamlinVIRTUS/workflow` or https://github.com/yyoshiaki/VIRTUS/blob/master/workflow/createindex.job.yaml .

Yoshi