Latest build of genomenexus/gn-annotation-pipeline:master is non-functional, even when using the toy example on https://docs.genomenexus.org/annotate-file

[pwaltman]

This tool used to work great, but the most recent build appears to be broken, no matter the input.

Whenever I try to use it, I get a SLF4J error. Because I kept getting these errors with my own MAFs, I decided to try using the toy example from https://docs.genomenexus.org/annotate-file, however, I get an error with that as well:

$ (echo -e "Chromosome\tStart_Position\tEnd_Position\tReference_Allele\tTumor_Seq_Allele1"; echo -e "7\t55220240\t55220240\tG\tT") > input.txt $ docker run -v ${PWD}:/wd genomenexus/gn-annotation-pipeline:master --filename /wd/input.txt --output-filename /wd/output.txt --isoform-override uniprot

SLF4J: Found binding in [jar:file:/genome-nexus-annotation-pipeline/annotationPipeline/target/annotationPipeline.jar!/BOOT-INF/lib/slf4j-log4j12-1.7.30.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/genome-nexus-annotation-pipeline/annotationPipeline/target/annotationPipeline.jar!/BOOT-INF/lib/logback-classic-1.2.3.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.slf4j.impl.Log4jLoggerFactory]
log4j:WARN No appenders could be found for logger (org.cbioportal.annotation.AnnotationPipeline).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
 RUNTIME: 0 secs.

[pwaltman]

After some research, it appears that there are multiple SLF4J bindings, which we see in the first 2 lines of the error message:

SLF4J: Found binding in [jar:file:/genome-nexus-annotation-pipeline/annotationPipeline/target/annotationPipeline.jar!/BOOT-INF/lib/logback-classic-1.2.3.jar!/org/slf4j/impl/StaticLoggerBinder.class]