Simon,
As you have probably noticed a new stable galaxy was released. It
includes 95% of what we discussed including this implicit check to see
if tool shed packages are enabled. Your help implementing, testing,
and driving these changes was greatly appreciated!
I couldn't however pull the trigger and mark packages resolved via
modules as "Installed" - so they will still appear to be in an error
state (though your check is in there and they won't attempt to be
installed, they will be just marked as errors). The upshot is you can
change this one line of code in your Galaxy instance to get the
behavior you desire (patch attached).
The reason I don't want to mark these packages as "Installed" is that
I am worried about Galaxy deployments that maybe want to use modules
are first but transition to tool shed packages down the road. I am
unsure what will happen if things are marked as "Installed" even if no
files corresponding to the installation exist. I think the state
NEVER_INSTALLED may be preferable - but I need to understand more
about what that means. For your own instance, if you are certainly
committed to using modules and not using the tool shed - it should be
easy to apply the above patch. Is this a fair compromise for the time
being?
Until I can resolve this last issue, the Trello card remains open, but
it should now be quite trivial to modify Galaxy to get the behavior
you desire and hopefully this can serve as a model for how others can
hook in other dependency resolution mechanisms.
I would be eager to hear how this experiment progresses and how you
feel about the implementation.
Thanks for your contributions,
-John
On Mon, Oct 14, 2013 at 8:33 PM, Guest, Simon
<simon.gu...@agresearch.co.nz> wrote:
> At Mon, 14 Oct 2013 20:22:06 -0500,
> John Chilton wrote:
>>
>> Simon,
>>
>> Very cool! I have two concerns. Rather than adding a new
>> configuration option I think I would prefer to just check the
>> configured dependency resolvers and then infer from them if the tool
>> shed will be used. The configuration option strikes me as having to
>> configure the same thing twice, and this change would make your setup
>> slightly easier. Do you have any objection to me reworking your patch
>> to do this? On the other hand, perhaps it is made more clear to the
>> deployer that they are definitely disabling tool dependency
>> installations if they have to add the explicit option this way.
>
> Hi John,
>
> I have no problem with you reworking it in that way. There are two reasons
> I didn't do that myself:
>
> 1. I would have had to change the interface to the dependency
> resolvers somehow to support this query, and I wasn't sure that was
> a good thing.
>
> 2. I wanted to make it explicit that toolshed package installation was
> disabled in this case, as I thought that would make it more likely
> this change gets accepted into the mainline.
>
> Whichever way you Greg and Dave are happy with is OK by me.
> Actually, I like your implicit approach better, so hope that's the one
> that gets agreed.
>
> cheers,
> Simon
# HG changeset patch
# User John Chilton <jmchil...@gmail.com>
# Date 1383627567 21600
# Mon Nov 04 22:59:27 2013 -0600
# Branch stable
# Node ID a278fe29f7217feb3145e785de92287f76455636
# Parent 5c789ab4144ac9db6c91b5646032894cae016309
Patch latest galaxy stable to mark packages resolved via modules when tool shed resolution disabled to be marked as INSTALLED in admin interface instead of ERROR.
diff -r 5c789ab4144a -r a278fe29f721 lib/tool_shed/util/common_install_util.py
--- a/lib/tool_shed/util/common_install_util.py Mon Nov 04 15:04:42 2013 -0500
+++ b/lib/tool_shed/util/common_install_util.py Mon Nov 04 22:59:27 2013 -0600
@@ -467,7 +467,7 @@
if app.toolbox.dependency_manager.find_dep( package_name, package_version, type='package') != INDETERMINATE_DEPENDENCY:
## TODO: Do something here such as marking it installed or
## configured externally.
- pass
+ status = app.model.ToolDependency.installation_status.INSTALLED
tool_dependency.status = status
else:
tool_dependency = install_package( app, elem, tool_shed_repository, tool_dependencies=tool_dependencies )
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