When you install a repository into Galaxy that contains workflows, you can
import the workflow into Galaxy. At the time the workflow is imported, the
import process checks to see if all required tools are available in Galaxy. If
not, a page is displayed with links to accessible Tool Sheds allowing the user
to search for missing required tools. I believe this still works, although
there have been some changes to the workflow framework over the past several
months, and I have not checked to see if this is still available. See
https://wiki.galaxyproject.org/ToolShedWorkflowSharing for more details.
This approach is basically a "hack" that I implemented several years ago. A
much better approach would be to enhance the workflow UI to include a feature
allowing the user to search Tool Sheds to discover and install missing tools
required by any workflow currently abvailable in the Galaxy instance.
Hopefully at some point soon something like this will be introduced.
Greg Von Kuster
On Mar 25, 2014, at 6:47 AM, "Lukasse, Pieter" <pieter.luka...@wur.nl> wrote:
> Hi Bjoern,
> I think you may have misunderstood me. What I mean is : instead of me having
> to add a tool_dependencies or repository_dependencies.xml to the workflows
> package, let Galaxy Tool Shed find these dependencies based on metadata
> available in the workflow itself.
> Best regards,
> -----Original Message-----
> From: Björn Grüning [mailto:bjoern.gruen...@gmail.com]
> Sent: dinsdag 25 maart 2014 11:43
> To: Lukasse, Pieter; Greg Von Kuster (g...@bx.psu.edu)
> Subject: Re: FW: prims workflows
> Hi Pieter,
> if I'm not misunderstood you, thats already possible:
> Have a look at:
> For an example.
> Am 25.03.2014 11:08, schrieb Lukasse, Pieter:
>> Hi Greg,
>> Do you have any plans of resolving the dependencies automatically when it
>> comes to workflows? E.g. I have a Tool Shed repository where I would like to
>> add workflows that are constructed using tools from different repositories.
>> It would be nice if you could let Tool Shed install the tools automatically
>> upon installation of the workflow. Any plans?
>> Best regards,
>> -----Original Message-----
>> From: Björn Grüning [mailto:bjoern.gruen...@gmail.com]
>> Sent: zaterdag 22 maart 2014 16:25
>> To: Lukasse, Pieter
>> Subject: prims workflows
>> Hi Pieter,
>> thanks for your prims Galaxy contributions.
>> Any chance to add a repository_dependencies.xml file to the workflow
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