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 env.sh (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.

-John

On Thu, Sep 26, 2013 at 11:39 PM, Guest, Simon
<simon.gu...@agresearch.co.nz> wrote:
> At Thu, 26 Sep 2013 22:03:09 -0400,
> Greg Von Kuster wrote:
>>
>> Hi John,
>>
>> On Sep 26, 2013, at 9:15 PM, John Chilton <chil...@msi.umn.edu> wrote:
>>
>> > I was not even thinking we needed to modify the tool shed to implement
>> > this. I was hoping (?) you could just modify:
>>
>> Nothing in the Tool Shed itself would be affected or require modification 
>> for this new feature as this is completely on the Galaxy side.
>>
>> >
>> > lib/galaxy/tools/deps/__init__.py
>> >
>> > to implement this. If some tool contains the tag
>> >
>> >  <requirement type="package" version="1.7.1">numpy</requirement>
>> >
>> > then if there is a manually installed tool_dependency in
>> > `tool_dependency_dir/numpy/1.7.1/env.sh` that would take precedence
>> > over the tool shed installed version (would that be something like
>> > `tool_dependency_dir/numpy/1.7.1/owner/name/changeset/env.sh`)? Let me
>> > know if this is way off base.
>>
>> This is a possibility perhaps, but there seems to be a potential weakness in 
>> that it doesn't require the Tool Dependency object to exist since the tool 
>> will function without a installed dependency from the Tool Shed.  Or, if the 
>> installed depndency s required, then it is meaningless because it won't be 
>> used.  If the former case, then the tool dependency cannot be shared via the 
>> Tool Shed's dependency mechanism because none of the relationships will be 
>> defined  since nothing is installed.  Wouldn't it be better to allow the 
>> Galaxy admin to point the ToolDependency object to a specified binary on 
>> disk?  In this way, all relationships defined by Tool Shed installations 
>> will work as expected, with all contained tools with that dependency point 
>> to that same shared location on disk.
>
> Hi Greg, John,
>
> What you are discussing is pretty close to what I am after, and what I
> am prepared to spend some time working on, if that can help.  This is
> what I have posted about a couple of times previously.  The option to
> use a pre-installed package rather than a Galaxy installed one I think
> would be very useful in general.  I think it can be done in a way that
> doesn't break the tool dependency model.
>
> I envisage providing access to existing programs on disk by loading
> the relevant environment module.  Platforms will differ greatly on
> where they have programs installed (usr/local/bwa-0.5.9,
> /usr/libexec/bwa-0.5.9, etc.).  However, we could arrange to have a
> conventionally named environment module available, so Galaxy just has
> to be told somehow to do a module load bwa/0.5.9, say, prior to
> trying to run that tool, which will then be found on the PATH.
>
> Hooking this in without killing the dependency on named and versioned
> toolshed repos could work like this.  In parallel with the repo sets
> named, e.g. package_bwa_0_5_9, which download and build the package,
> we have a set named like native_package_bwa_0_5_9.  This could have a
> tool_dependencies.xml file like this:
>
> <?xml version="1.0"?>
> <tool_dependency>
>     <native_package name="bwa" version="0.5.9">
>         <actions>
>             <action type="load_module">
>                 <module name="bwa" version="0.5.9"</module>
>             </action>
>         </actions>
>         <readme>
> Uses native BWA via environment module bwa/0.5.9
>         </readme>
>     </native_package>
> </tool_dependency>
>
> What this does is ensure that any repo which requires version 0.5.9 of
> bwa can have this dependency resolved by either package_bwa_0_5_9, or
> native_package_bwa_0_5_9.
>
> I envisage a Galaxy configuration setting that enables native package
> and/or Galaxy package dependency resolution, and which one should be
> preferred.  Of course, if one of these has been manually installed, it
> will be used as is.
>
> I would really like to be able to install tools from the toolshed, and
> have them resolve their dependencies automatically using my
> preinstalled application suite.  I see that would also meet the needs
> being discussed here.
>
> How does that sound?
>
> cheers,
> Simon
>
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