I am observing some difficulties running a custom tool (processing an sff file). It shows up in Galaxy, runs and its three output files are given back. Only one of them is only showing the first 12 lines of many more...
More symptoms:
The corrupted file is written successfully to disk as temp file in the galaxy tmp directory
Something goes wrong while transfering the file to the galaxy data dir (files/001), because while the tool is running the dataset_XX file is shown (as empty file), but after the other outputs are moved this file is gone
in galaxy only a snippet is shown, while the actual datafile is not on disk
I would be happy to receive feedback on how to start debugging and solving this issue.
Thanks!
Mattias
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Bioinformatician
Netherlands Institute of Ecology (NIOO-KNAW)
Wageningen, the Netherlands