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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