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.

>> 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?

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? ;)

Thanks,

Peter
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