Re: [galaxy-dev] Portable tool identifiers in workflows
On Thu, Jun 13, 2013 at 6:34 PM, Greg Von Kuster <greg@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
Hi Peter, On Jun 13, 2013, at 4:14 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thu, Jun 13, 2013 at 6:34 PM, Greg Von Kuster <greg@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,
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On Fri, Jun 14, 2013 at 1:40 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Peter,
On Jun 13, 2013, at 4:14 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thu, Jun 13, 2013 at 6:34 PM, Greg Von Kuster <greg@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.
<cut>
For anyone else interested, some good news from Dannon: On Fri, Jun 21, 2013 at 10:27 AM, Dannon Baker wrote:
All those issues in the trello card should be resolved now, importing workflows should work as expected.
-Dannon
Excellent news - thank you all :) Peter
On Fri, Jun 21, 2013 at 2:21 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Fri, Jun 14, 2013 at 1:40 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:
Hi Peter,
On Jun 13, 2013, at 4:14 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thu, Jun 13, 2013 at 6:34 PM, Greg Von Kuster <greg@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.
<cut>
For anyone else interested, some good news from Dannon:
On Fri, Jun 21, 2013 at 10:27 AM, Dannon Baker wrote:
All those issues in the trello card should be resolved now, importing workflows should work as expected.
-Dannon
Excellent news - thank you all :)
Peter
Or possibly not quite yet, new Trello card: https://trello.com/card/workflows-do-not-properly-handle-tool-shed-generated... Peter
participants (2)
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Greg Von Kuster -
Peter Cock