At Fri, 27 Sep 2013 00:23:37 -0500,
John Chilton wrote:
> Simon,
> What is the advantage of putting that XML definition in the tool shed?
> It is not 100% true because of prior_install_required dependencies,
> but for the most part sourcing/load the environment for tools is a
> Galaxy problem, not so much a tool shed one. What if we did this
> instead?
> Add an option to Galaxy's universe_wsgi.ini with the following default:
> tool_dependency_resolution_order = gx_package_manual, gx_package_toolshed
> Which essentially implements my idea above, with James' additional
> configuration. But which can be overridden as:
> tool_dependency_resolution_order = plugin_module, gx_package_manual,
> gx_package_toolshed
> If set this way then placing <requirement
> package="0.5.9">bwa</requirement> in a tool will result in the module
> bwa/0.5.9 being loaded if it is 'avail'able, else it will check for a
> manually installed (which is where MSI is currently putting its
> module loads), and else it will fallback to source the tool shed
> installed dependency.
> I feel like this will give you everything you want without any extra
> XML or configuration. Let me know if I am wrong.

Hi John,

I think you're right.  Your scheme is neater than what I was
proposing.  The extra flexibility I was aiming at via some toolshed
XML stuff appears not to be necessary upon further reflection.  (I
wanted to ensure a Galaxy admin could just install some RPMs, install
a toolshed tool, and have everything resolve nicely.  You seem to have
achieved that with your scheme.)

I haven't had a chance to try your code yet, but as soon as I can I
will do so, and get back to you.

If I leave out gx_package_toolshed altogether from
tool_dependency_resolution_order, will the tool installation in Galaxy
simply fail with a nice error message if the environment module and/or files are not found?  (This is what I would like, as it would
serve as a prompt to the Galaxy admin to install some extra RPMs or

Will this also work for those toolshed packages which bundle their
package definitions (to download, make and install the tool
dependency) along with their wrappers?

Thanks for working on this.


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