Error

[SamKap-2]

Could you throw some light on this error bpipe.PipelineError: Error evaluating script '~/ximmer/eval/pipeline/config.groovy': No such property: HGFA for class: ~/ximmer/eval/pipeline/config.groovy at bpipe.Pipeline$_loadExternalStagesFromPathList_closure14.doCall(Pipeline.groovy:1027) at bpipe.Pipeline.loadExternalStagesFromPathList(Pipeline.groovy:1000) at bpipe.Pipeline.loadExternalStagesFromPaths(Pipeline.groovy:982) at bpipe.Pipeline.loadExternalStagesFromPaths(Pipeline.groovy) at bpipe.Pipeline.load(Pipeline.groovy:1107) at exome_cnv_pipeline.groovy.run(exome_cnv_pipeline.groovy:30) at exome_cnv_pipeline.groovy$run.call(Unknown Source) at bpipe.Runner.main(Runner.groovy:439)

[ssadedin]

Apologies, it looks like the installer is not setting this up properly.

I'll get a fix in for it, but in the meantime, could you try editing the file

~/ximmer/eval/pipeline/config.groovy

And in there, put a line like so:

HGFA="/path/to/genome/reference.fa"

Where you need to replace that reference with the same reference that your BAM files are aligned to.

[SamKap-2]

Thanks Simon