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 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.



Netherlands Institute of Ecology (NIOO-KNAW)
Wageningen, the Netherlands
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