Thanks Martin, that helps me out.  However, the issue I'm running into is
that it seems like specific revisions in my repository suite definition are
being ignored and it's only using the latest one.

I think what may be happening is as follows.

In my repository suite I have a dependency like:

<repository changeset_revision="0" name="package_x" owner="devteam"
toolshed="http://toolshed.g2.bx.psu.edu"; />

Now, "package_x" defines dependencies for tools in a
"tool_dependencies.xml" file.  And it has been updated to a newer revision,
"1".

Looking through the toolshed, it looks like revision "0" for "package_x"
isn't being set as an installable revision.  So, when installing my older
repository dependency suite, it's ignoring revision "0" and just installing
revision "1".

Is there any way to force it to install revision "0" of package_x?  Should
I never be updating the repositories for tool dependencies?

This was all being tested out with toolshed tag "v15.05.1".

Thanks,

Aaron



On Wed, Nov 4, 2015 at 10:28 AM, Martin Čech <mar...@bx.psu.edu> wrote:

> Hi Aaron,
>
> we touched this recently here:
> https://github.com/galaxyproject/tools-devteam/pull/267
>
> I believe that if you specify the repository_dependencies.xml of your
> suite in the following way:
>
> <repositories>
> <repository changeset_revision="f2ab5b44870d"
> name="fasta_clipping_histogram" owner="devteam" toolshed="
> http://toolshed.g2.bx.psu.edu"; />
>
> you will pin the exact revision of the tool (fasta_clipping_histogram
> here) to that suite. Then you can have suite_fastx_toolkit_0_0_13 and
> suite_fastx_toolkit_0_0_9 repositories which will install the requested
> versions of the tools.
>
> M.
>
> On Wed, Nov 4, 2015 at 10:47 AM Aaron Petkau <aaron.pet...@gmail.com>
> wrote:
>
>> Okay, thanks Dave.  That makes sense.  Moving forward I'll just make a
>> new suite with a version number in the name.
>>
>> Another question, does the same apply for tool dependency definitions?
>> I've upgraded a suite of tools + dependency definitions, and now even if I
>> make a new repository suite (to allow installing of my old set of tools,
>> revision 0 in my example) it's installing the newer commit in one tool
>> dependency definition repository.
>>
>> Thanks,
>>
>> Aaron
>>
>> On Mon, Nov 2, 2015 at 7:59 AM, Dave Bouvier <d...@bx.psu.edu> wrote:
>>
>>> Aaron,
>>>
>>> Repository suite definitions are designed to only allow the latest
>>> revision to be installable. My recommendation in this case would be to
>>> define two separate suites tagged in some descriptive way, so the
>>> individual use cases would have their appropriate suites.
>>>
>>> -
>>> Dave Bouvier
>>> http://galaxyproject.org
>>> http://usegalaxy.org
>>>
>>>
>>> On 10/29/2015 02:23 PM, Aaron Petkau wrote:
>>>
>>>> Hello,
>>>>
>>>> I'm running into some issues with maintaining multiple installable
>>>> revisions for a repository suite and I'm not sure if there's something
>>>> I've missed.
>>>>
>>>> I have a local toolshed where I'm maintaining my tools, and I have a
>>>> repository suite definition, defining a number of dependencies.  So, I
>>>> have:
>>>>
>>>> suite_X (mercurial revision 0):
>>>>     Dependency A
>>>>     Dependency B
>>>>
>>>> I updated "suite_X" and changed the dependencies:
>>>>
>>>> suite_X (mercurial revision 1):
>>>>      Dependency A
>>>>      Dependency B
>>>>      Dependency C
>>>>
>>>> I would like to have both mercurial revision 0 and 1 installable in
>>>> Galaxy, but only revision 1 (the latest) is showing up as installable.
>>>> I found documentation at
>>>> https://wiki.galaxyproject.org/RepositoryRevisions but this seems to
>>>> only cover a repository containing a single tool, not a suite of tools.
>>>>
>>>> Is there something I'm doing wrong or some setting I have to change
>>>> here?  My toolshed is running with Galaxy tag "v15.07".
>>>>
>>>> Thanks,
>>>>
>>>> Aaron
>>>>
>>>>
>>>> ___________________________________________________________
>>>> Please keep all replies on the list by using "reply all"
>>>> in your mail client.  To manage your subscriptions to this
>>>> and other Galaxy lists, please use the interface at:
>>>>    https://lists.galaxyproject.org/
>>>>
>>>> To search Galaxy mailing lists use the unified search at:
>>>>    http://galaxyproject.org/search/mailinglists/
>>>>
>>>>
>> ___________________________________________________________
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Reply via email to