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genome-nexus / genome-nexus-annotation-pipeline

Library and tool for annotating MAF files using Genome Nexus Webserver API
MIT License
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Add new flag for logging verbosity and log output location #247

Open leexgh opened 1 year ago

leexgh commented 1 year ago

The current logging is a bit complicated to see if running through docker. Add new flags for logging:

  1. set verbosity to print out logging info to command line: e.g. --verbosity=verbose
  2. set log file path: e.g. --output-log=output.log
johnoooh commented 11 months ago

This caused an issue at the hackathon where, when working in a singularity container, log files cannot be written as singularity creates a read only file system. log4j:ERROR setFile(null,true) call failed. java.io.FileNotFoundException: /genome-nexus-annotation-pipeline/logs/genome-nexus-annotation-pipeline.log (No such file or directory)

The proposed feature would allow the pipeline to be run using singularity and on the HPC as docker is not supported on juno.

hweej commented 2 months ago

I will reference this https://github.com/nextflow-io/nextflow/discussions/4260 as a docker workaround for now as this can explicitly set by specifying the volume mounts via containerOptions

It could be preferable for annotationPipeline.jar to allow dumping of the log to stdout instead...

Notes: Still doesn't solve singularity read-only filesystem yet...