On Fri, Feb 27, 2015 at 8:58 PM, Dooley, Damion <damion.doo...@bccdc.ca> wrote:
> First, hey Peter, thanks for input!  I'd seen the explicit piping before,
> couldn't remember its format though; I will switch to it.
> Well, after a morning of testing, I see the test system is actually
> finding the repeat section variables.  It looks like its error
> "Parameter filter_column requires a value, but has no legal
> values defined" points to the fact that it can't process any
> option list having <options from_data_table="[whatever table we got]"> .
> I'd assumed Planemo in its test setup would install the tool's data
> tables, but now I see it is still on John's enhancement list. So I'll
> table those tests until that's a go.
> I guess manually setting up the data tables in galaxy won't solve
> that for planemo?
> *************************
> I'm still stuck trying to get tool test directly in a fresh copy of
> Galaxy.  I edit config/tool_conf.xml.sample to have
>   <section id="testing" name="TESTING">
>     <tool file="TESTING/blast_reporting/blast_reporting.xml" />
>   </section>
> And I run "tests.sh -id blast_reporting" (with Galaxy as owner
> of tool folder):

While the tests used to use tool_conf.xml.sample last year
(or even longer ago?) this was switched to using the main
tool_conf.xml instead. This is much easier for testing what
you actually have installed.

If I've guessed wrong, watch the run_tests.sh output to see
which tools are loaded - and make sure your tool loads OK
(and for example doesn't fail with an XML error or something).

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