Hi Peter,

On Jun 13, 2013, at 4:14 PM, Peter Cock <p.j.a.c...@googlemail.com> wrote:

> On Thu, Jun 13, 2013 at 6:34 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
>> Hello Peter,
>> 
>> Unfortunately, workflows are currently not very compatible with
>> the tool shed - there is a Trello card that details the issues here:
>> 
>> https://trello.com/card/workflow-issues/506338ce32ae458f6d15e4b3/692
>> 
> 
> Thanks Greg - I see that Trello card is "in progress", but
> it covers quite a broad range of issues.


These long standing issues are the reason I am not marketing workflow use in 
the tool shed in a more prominent way.  You may have noticed that importing 
workflows from an installed tool shed repository into Galaxy is not a simple 
process.  I have not worked on streamlining this process (or other workflow 
related features for the tool shed) due to these same issues.


> 
>>> So, does Galaxy handle old fashioned tool identifiers and the
>>> newer toolshed-tool-identifiers gracefully in a situation like this?
>> 
>> Unfortunately this does not currently work ...
>> 
>>> Do I need to update the *.ga files to use toolshed-tool-ids? If
>>> I did that, would it break the workflow on any Galaxy instance
>>> (like ours) where the tools were installed manually?
>> 
>> Yes, you would currently need to update the workflows to use
>> toolshed-tool-ids, and your statement regarding the workflow
>> not working with older tools is correct.
> 
> So in the short term the best thing to do is to edit these workflows
> as posted on the Tool Shed (easy enough as the *.ga files are
> plain text) to replace the tool identifiers?


Yes, this is probably the only way to make this work.


> 
> What would be the easiest way to work out the desired id form
> from a tool repository page? Other than reinstalling the tools
> locally but from the Tool Shed this time? ;)


The tool ids should be the name-spaced guid that is automatically defined for 
each tool when it is uploaded to a tool shed repository.  The guid consists of 
these components:

<tool shed host>/repos/<repository owner>/<repository name>/<tool id>/<tool 
version>

For example, your blast2go tool in the test tool shed has the following guid:

testtoolshed.g2.bx.psu.edu/repos/peterjc/blast2go/blast2go/0.0.8

                     
> 
> Thanks,
> 
> Peter
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