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ssadedin / ximmer

Ximmer is a system for CNV calling on exome and targeted genomic sequencing
http://ssadedin.github.io/ximmer/
GNU Lesser General Public License v2.1
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Error #9

Open SamKap-2 opened 6 years ago

SamKap-2 commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

Thanks Simon