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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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Orange for panel output #404

Closed davidvanzessen closed 1 year ago

davidvanzessen commented 1 year ago

Hello,

I've a question about using Orange after the update to allow for it to be used on the panel analysis output. The readme gives a convenient example how to run Orange for this use case.

But when I execute the command (after filling in the paths to our output directories/files of course), it gives an error:
org.apache.commons.cli.UnrecognizedOptionException: Unrecognized option: -purple_data_directory

I double checked, and am using the latest (1.10) version of Orange. I've tried to remove/add arguments to make it work, but so far it keeps popping up errors...

Hope I'm not doing something obvious wrong, thanks in advance.

kduyvesteyn commented 1 year ago

1.10 is not the latest version, tumor-only has been added in 2.0 and TARGETED mode in 2.3

See also https://github.com/hartwigmedical/hmftools/tree/master/orange