Hello Björn,

I've added your comments to the following Trello card.  I'm doing some thinking 
on this issue to make sure I come up with the optimal solution.  Thanks for the 
valuable input!

https://trello.com/card/toolshed-enable-dependency-definitions-across-tool-sheds/506338ce32ae458f6d15e4b3/838

Greg Von Kuster

On May 7, 2013, at 5:49 AM, Björn Grüning wrote:

> Hi,
> 
> nice work Ira! That problem also bothers me. I have written a similar
> script in python, but its not documented ;) I really think a more
> advanced solution like Peter's are needed midterm.
> 
> To fix the revision problems: What about leaving the revision tag blank
> means that the toolshed should insert the latest revision of a tool
> dependency during upload.
> 
> For me the vast majority of repo uploads referring to the latest
> dependencies of other repo's. So I ending up with uploading one repo,
> running my script to insert the new revision tag, uploading the second,
> rerun the script and so on ...
> 
> Ciao,
> Bjoern
> 
>> Helo Peter and Ira,
>> 
>> These are great ideas and contributions, and I'll make sure to incorporate 
>> some version of them into the Tool Shed framework as soon as possible.  I've 
>> created the following Trello card for this.
>> 
>> Thanks!
>> 
>> https://trello.com/card/toolshed-enable-dependency-definitions-across-tool-sheds/506338ce32ae458f6d15e4b3/838
>> 
>> 
>> On May 6, 2013, at 11:05 AM, Peter Cock wrote:
>> 
>>> On Thu, May 2, 2013 at 10:24 AM, Peter Cock <p.j.a.c...@googlemail.com> 
>>> wrote:
>>>> On Thu, May 2, 2013 at 7:16 AM, Ira Cooke <iraco...@gmail.com> wrote:
>>>>> Hi all,
>>>>> 
>>>>> I've written a script to help deal with the problem of maintaining 
>>>>> toolshed tools
>>>>> across multiple toolsheds (eg test and release)
>>>>> 
>>>>> The problem I encountered was that switching between test and production
>>>>> versions of a suite of tools can be quite painful because every repository
>>>>> definition like this
>>>>> 
>>>>> <repository toolshed="http://toolshed.g2.bx.psu.edu"; 
>>>>> name="proteomics_datatypes" owner="iracooke" 
>>>>> changeset_revision="463328a6967f"/>
>>>>> 
>>>>> needs to be updated to a different toolshed url and (by extension) a 
>>>>> different
>>>>> changeset revision.
>>>>> 
>>>>> The idea with this script is that you should be able to point it at a 
>>>>> directory
>>>>> containing a toolshed repository and it will create a copy of that 
>>>>> repository
>>>>> in which the toolshed urls (and changeset revisions) have been updated
>>>>> to correct values for a different toolshed.
>>>>> 
>>>>> I'm not sure how others are dealing with this issue (perhaps there is 
>>>>> another
>>>>> easier way) .. but I've found this helped me alot so I thought I'd share
>>>>> 
>>>>> https://bitbucket.org/iracooke/galaxy_repo_bundler/
>>>>> 
>>>>> Cheers
>>>>> Ira
>>>> 
>>>> Thanks Ira,
>>>> 
>>>> I've not made as heavy use of inter-repository dependencies as you, but
>>>> thus far I have ignored the problem (only a couple of my repositories are
>>>> affected), in the hope this limitation will be fixed sooner rather than 
>>>> later.
>>>> 
>>>> Peter
>>> 
>>> Thinking out loud, another way to solve this would be to allow multiple
>>> equivalent <repository> entries as a group where any one would be OK.
>>> 
>>> e.g. For v0.0.5 of my seq_filter_by_id tool,
>>> 
>>> <repository toolshed="http://toolshed.g2.bx.psu.edu"; owner="peterjc"
>>> name="seq_filter_by_id" changeset_revision="abdd608c869b"/>
>>> for http://toolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id/abdd608c869b
>>> 
>>> or:
>>> 
>>> <repository toolshed="http://testtoolshed.g2.bx.psu.edu";
>>> owner="peterjc" name="seq_filter_by_id"
>>> changeset_revision="66d1ca92fb38"/>
>>> for 
>>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id/66d1ca92fb38
>>> 
>>> Something like this maybe?:
>>> 
>>> <any_one_of>
>>> <repository toolshed="http://toolshed.g2.bx.psu.edu"; owner="peterjc"
>>> name="seq_filter_by_id" changeset_revision="abdd608c869b"/>
>>> <repository toolshed="http://testtoolshed.g2.bx.psu.edu";
>>> owner="peterjc" name="seq_filter_by_id"
>>> changeset_revision="66d1ca92fb38"/>
>>> </any_one_of>
>>> 
>>> Of course more generally we might also post this on a local public Tool
>>> Shed as well. The point is then the same repository_dependencies.xml
>>> could be used on either tool shed without modification.
>>> 
>>> Fixing declaring a dependency on an external Tool Shed would be better -
>>> but perhaps we'll need both or some sort of mirroring federated system
>>> in the long term?
>>> 
>>> Peter
>>> ___________________________________________________________
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>> 
>> 
>> ___________________________________________________________
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> 
> 
> 


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