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TheJacksonLaboratory / LIRICAL

LIkelihood Ratio Interpretation of Clinical AbnormaLities
https://thejacksonlaboratory.github.io/LIRICAL/stable
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[ERROR] Expected a command, got vcf #487

Closed vidarmehr closed 4 years ago

vidarmehr commented 4 years ago

@pnrobinson @justaddcoffee

I got the following error when I ran:

$ java -jar LIRICAL.jar vcf -y example.yml

The yml file that I used is simple.yml in /LIRICAL/src/test/resources/yaml

SLF4J: Class path contains multiple SLF4J bindings. SLF4J: Found binding in [jar:file:/Users/ravanv/Documents/IntelliJ_projects/LIRICAL/target/LIRICAL.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: Found binding in [jar:file:/Users/ravanv/Documents/IntelliJ_projects/LIRICAL/target/lib/log4j-slf4j-impl-2.12.0.jar!/org/slf4j/impl/StaticLoggerBinder.class] SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation. SLF4J: Actual binding is of type [org.apache.logging.slf4j.Log4jLoggerFactory] [ERROR] Expected a command, got vcf [ERROR] your command: vcf -y /Users/ravanv/Documents/IntelliJ_projects/LIRICAL/src/test/resources/yaml/simple.yml [ERROR] enter java -jar LIRICAL.jar -h for more information.

justaddcoffee commented 4 years ago

I think that should be:

java -jar LIRICAL.jar yaml -y example.yml

justaddcoffee commented 4 years ago

I see why you used the command you did - this command: java -jar LIRICAL.jar vcf -y example.yml on this page https://lirical.readthedocs.io/en/latest/yaml-hpo.html is incorrect

justaddcoffee commented 4 years ago

Fixed here https://github.com/TheJacksonLaboratory/LIRICAL/pull/486

vidarmehr commented 4 years ago

I think that should be:

java -jar LIRICAL.jar yaml -y example.yml

Yes. Thank you very much!

justaddcoffee commented 4 years ago

No problem Vida!