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gvlproject / gvl.ansible.playbook

Playbook for building the Genomics Virtual Laboratory
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GenomeSpace Importer - Galaxy workflow renaming issue #57

Open igormakunin opened 8 years ago

igormakunin commented 8 years ago

I cannot rename files imported by GenomeSpace Importer in Galaxy workflow. I have a Galaxy workflow with Importer. I set up the datatype and a new name for the dataset through the Workflow Editor. GenomeSpace Importer creates the specified name during the upload, but replaced it with default 'GenomeSpace importer on...' after completion of the upload.

nuwang commented 7 years ago

Unfortunately, this does not appear to be doable. This is because, although the initial dataset name can be specified within the workflow editor and is set by Galaxy as the tool runs, this same does not appear to be accessible to the tool wrapper when the tool starts running.

As a result, the GenomeSpace importer is forced to provide "GenomeSpace importer on..." following the convention of other tools, as it's not guaranteed that the dataset will have a name if this is not done.

The reason the name is probably not accessible by the wrapper is because the GenomeSpace importer is a "data_source" tool, and not a conventional tool, and therefore, Galaxy's handling of naming etc. is very different. I think this boils down to the behaviour of Galaxy, and is arguably a bug. Data source handling in Galaxy is pretty inconsistent anyway.