I installed a local instance of Galaxy, and (i believe) downloaded all of
the dependencies, indexes, and modified the appropriate .loc files.  Pretty
much all of the tools work, except for Bowtie2. (I installed the bowtie
tool, and it works perfectly)

The bowtie2 sequence assembler completes with appropriate output from the
command-line, but not from the WEB-GUI interface.

When you run Bowtie2 from the web-GUI, it completes almost immediately, not
with an error, but with a 62byte bam file. The output box in the gui
indicates the file contents are 'binary bam alignments file'.

For the record, I installed the bowtie2 example lamda indexes in Galaxy and
modified the loc file. After running the example FQ files  through the
WEB-GUI I received the same 62Byte output, indicating it's not a file or
index problem. Running this example on the command-line completes as

Has anyone seen this. I'm sure I did something stupid somewhere, I just
can't seem to find it.  Any assistance would be appreciated.

Kind regards,

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