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ohsu-comp-bio / cwl-tes

cwl-tes submits your tasks to a TES server. Task submission is parallelized when possible.
Apache License 2.0
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Input download not supported by storage #20

Closed azat-badretdin closed 6 years ago

azat-badretdin commented 6 years ago

I am trying to test NCBI PGAP pipeline with cwl-test, and I got this from funnel

{"attempt":0,"error":"Input download not supported by storage: could not find matching storage system for: file:///panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/home/badrazat/github/repos/pgap/MG37/ASM2732v1.annotation.nucleotide.1.fa\nlocalStorage: can't access file, path is not in allowed directories: file:///panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/home/badrazat/github/repos/pgap/MG37/ASM2732v1.annotation.nucleotide.1.fa","index":0,"level":"error","msg":"System error","ns":"local","taskID":"bcr7t15bhkg3snik2pn0","time":"2018-06-29T18:46:28Z","timestamp":"2018-06-29T18:46:28.893110876Z"}

How do I tell funnel to recognize local files?

adamstruck commented 6 years ago

You need to configure the local storage module in funnel. Check out the docs here: https://ohsu-comp-bio.github.io/funnel/docs/storage/local/

adamstruck commented 6 years ago

@azat-badretdin were you able to get Funnel working?

adamstruck commented 6 years ago

Closing due to inactivity and since this is a Funnel config issue rather than a cwl-tes issue.