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phnmnl / container-galaxy-k8s-runtime

PhenoMeNal runtime for Galaxy running inside a container orchestrator
Apache License 2.0
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mzML data type not immediately recognised in a fresh installation #205

Closed sneumann closed 6 years ago

sneumann commented 6 years ago

Hi, on a freshly installed instance based on 17.09 galaxy-stable, I upload an mzML file (detect datatype=auto), the metadata says it is format mzml, but the xcms tool (and iirc also OpenMS) don't recognize that as valid input. Then I edit and change the datatype from mzml to mzml (sic!) and things work. Any mzML from the same experiment uploaded afterwards is available for xcms right away. My suspicion would be that the mzML is not correctly attached to the history item, that could be a Galaxy issue. Let's re-visit once we are on 18.01. Yours, Steffen

ilveroluca commented 6 years ago

This issue seems to be solved with the updated version of Galaxy we're deploying with Dalcotidine. I just verified that it works on minikube with the "IPO for xcmsSet" tool using our current (almost RC2) PhenoMeNal deployment.

Closing the issue.