Forwarding back to the list which had been offline and
seemed to be missing these two emails...

---------- Forwarded message ----------
From: Greg Von Kuster <g...@bx.psu.edu>
Date: Thu, Jun 13, 2013 at 6:34 PM
Subject: Re: Portable tool identifiers in workflows
To: Peter Cock <p.j.a.c...@googlemail.com>
Cc: Galaxy Dev <galaxy-...@bx.psu.edu>, Björn Grüning
<bjoern.gruen...@pharmazie.uni-freiburg.de>


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

See my inline comments below.


On Jun 13, 2013, at 7:13 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:

> Hi Greg,
>
> I've recent uploaded a couple of workflows to the Tool Shed,
> http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list/
> http://toolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow
>
> The *.ga files where created by saving the workflow from our
> local Galaxy instance. I then wrote a repository_dependencies.xml
> file, a README file, made a tar ball, and uploaded this to the
> Tool Shed.
>
> Perhaps unusually the tools were installed manually rather than
> via the Tool Shed. This is basically because our Galaxy instance
> pre-dates the new hg based Tool Shed, and I was already installing
> locally developed tools this way.
>
> This has a potential implication in the form of the tool identifiers,
> drawn to my attention by Björn:
>
> On Thu, Jun 13, 2013 at 10:54 AM, Björn Grüning wrote:
>>
>> ... I'm just asking because your
>> tool-ids in the ga file are not toolshed-tool-ids. So I'm curious if
>> that can work.
>>
>> I will bug Greg.
>
> 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 - this is related to the
3rd item in the above Trello card:

Workflows do not consider tool version lineage when inspecting the
Galaxy tools_by_id in-memory dictionary, so tools that should be
discovered for a workflow are not.

>
> 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.  This again is related to the 3rd
item in the above Trello card:

Workflows do not consider tool version lineage when inspecting the
Galaxy tools_by_id in-memory dictionary, so tools that should be
discovered for a workflow are not.


>
> Unfortunately from the point of view of testing, these first two
> workflows both require a Tool Shed repository dependency
> which is non-auto-installable (propriety licensing).
>
> Thanks,
>
> Peter
>

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