Forwarding back to the list which had been offline and seemed to be missing these two emails... ---------- Forwarded message ---------- From: Greg Von Kuster <greg@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.cock@googlemail.com> Cc: Galaxy Dev <galaxy-dev@bx.psu.edu>, Björn Grüning <bjoern.gruening@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.cock@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