On Tue, Oct 20, 2015 at 10:01 AM, Tiago Rodrigues Antao <t...@popgen.net> wrote:
> Hi,
>
> I am afraid that I might be overlooking something obvious but...
>
> I am trying to add a few tools to the RAD-Seq portfolio of Galaxy. For
> that effect I am designing a few package wrappers. My problem is to
> understand the best practice to develop wrappers for dependencies of
> external tools.
>
> For normal tools, that is quite easy: one uses the galaxy/tool/XXX
> to do all development and testing.
>
> But for dependency wrappers, the only solution that I have found is to
> upload the wrapper to a toolshed and installing it via the admin
> interface... This is cumbersome. Is there any way to test/develop a
> package wrapper so that I can test tool_dependencies.xml without
> uploading it to a toolshed and installing it from there?
>
> Thanks,
> Tiago

Hi Tiago,

If you've not seen planemo, I suggest you have a look at
https://github.com/galaxyproject/planemo and
https://github.com/galaxyproject/planemo or the slides John
gave at GCC 2015:

http://gcc2015.tsl.ac.uk/abstracts/#Planemo_8211_A_Galaxy_Tool_SDK

For tool testing during development this ought to work:

planemo test path/to/your/tool

For tool dependency testing, I used to rely on the nightly tests
run on the main and Test Tool Shed, currently unavailable. One
option here is to run your own local tool shed just for development,
but the Test Tool Shed is a reasonable substitute. See also:

planemo shed_test --help

I recently started work on the new "planemo dependency_script"
which attempts to parse tool_dependencies.xml into a bash
script - that is still a work in progress but might help here too:

https://github.com/galaxyproject/planemo/issues/303
https://github.com/galaxyproject/planemo/commit/f798c7e29b2276ce68b828e72fc6a6460c73792b

See also https://github.com/galaxyproject/planemo/issues/19
for the wider issue of testing tool_dependencies.xml with
planemo without a tool shed.

Regards,

Peter
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