interoperabilty between Galaxy and other workflow environments
Dear galaxy devs, Is there any possibility (tool, script) to easily _convert a program description from a xml format into another_ (Mobyle to Galaxy, or Taverna to Galaxy for example) ? And I wonder as well how is the interoperability between these different tools for the _workflows_ (export - import). Thanks for your help, Loraine -- Loraine Brillet Service Informatique et Genomique Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences) Station Biologique de Roscoff FR 2424 CNRS UPMC Place Georges Teissier 29682 Roscoff Cedex tel: ++33 (0)2 98 29 25 50 fax: ++33 (0)2 98 29 23 24 email: loraine.brillet@sb-roscoff.fr http://www.sb-roscoff.fr http://www.sb-roscoff.fr/abims/
Hi Loraine,
Is there any possibility (tool, script) to easily _convert a program description from a xml format into another_ (Mobyle to Galaxy, or Taverna to Galaxy for example) ? And I wonder as well how is the interoperability between these different tools for the _workflows_ (export - import).
This is planned functionality, but there are multiple Galaxy workflow issues that take precedence over interoperability with other systems. In particular, there's active development right now to enable workflows and tools to be imported (intp a local Galaxy instance), exported (from a local Galaxy instance), and stored on a community website. Once this functionality is in place and tested, we can extend it to work with other systems. Thanks, J.
Would it be possible to include a direct link from the Workflow page to the page of published workflows? This seems like the most logical way for our galaxy users to collect workflows we have created for them or previously for other people. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
Hi Shaun,
Would it be possible to include a direct link from the Workflow page to the page of published workflows? This seems like the most logical way for our galaxy users to collect workflows we have created for them or previously for other people.
Yes, links are needed to Galaxy's published items. We're talking about where to put the links, and we'll put together something next week. Thanks for the feedback. Best, J.
Just to follow-up, it is very *possible*. Tool configurations are in a documented XML format. Workflows are currently exportable as a json (proprietary format), and an XML format will be defined soon. At the moment, we do have plans to implement specific conversion programs however. On May 5, 2010, at 8:26 AM, Jeremy Goecks wrote:
Is there any possibility (tool, script) to easily _convert a program description from a xml format into another_ (Mobyle to Galaxy, or Taverna to Galaxy for example) ? And I wonder as well how is the interoperability between these different tools for the _workflows_ (export - import).
Thanks for your answer. One more question: Is there any data warehouse where xml program description for galaxy are left and shared ? Regards Loraine Jeremy Goecks wrote:
Hi Loraine,
Is there any possibility (tool, script) to easily _convert a program description from a xml format into another_ (Mobyle to Galaxy, or Taverna to Galaxy for example) ? And I wonder as well how is the interoperability between these different tools for the _workflows_ (export - import).
This is planned functionality, but there are multiple Galaxy workflow issues that take precedence over interoperability with other systems. In particular, there's active development right now to enable workflows and tools to be imported (intp a local Galaxy instance), exported (from a local Galaxy instance), and stored on a community website. Once this functionality is in place and tested, we can extend it to work with other systems.
Thanks, J.
-- Loraine Brillet Service Informatique et Genomique Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences) Station Biologique de Roscoff FR 2424 CNRS UPMC Place Georges Teissier 29682 Roscoff Cedex tel: ++33 (0)2 98 29 25 50 fax: ++33 (0)2 98 29 23 24 email: loraine.brillet@sb-roscoff.fr http://www.sb-roscoff.fr http://www.sb-roscoff.fr/abims/
We're working on such a place where users can share their tools (and workflows), and the community can provide feedback. In the meantime, we recommend using the "ThirdPartyTools" page on the galaxy wiki. On May 7, 2010, at 5:02 AM, Loraine Brillet wrote:
Is there any data warehouse where xml program description for galaxy are left and shared ?
thanks! Could you please give me the url for this web page, I can't find it. Loraine James Taylor wrote:
We're working on such a place where users can share their tools (and workflows), and the community can provide feedback.
In the meantime, we recommend using the "ThirdPartyTools" page on the galaxy wiki.
On May 7, 2010, at 5:02 AM, Loraine Brillet wrote:
Is there any data warehouse where xml program description for galaxy are left and shared ?
-- Loraine Brillet Service Informatique et Genomique Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences) Station Biologique de Roscoff FR 2424 CNRS UPMC Place Georges Teissier 29682 Roscoff Cedex tel: ++33 (0)2 98 29 25 50 fax: ++33 (0)2 98 29 23 24 email: loraine.brillet@sb-roscoff.fr http://www.sb-roscoff.fr http://www.sb-roscoff.fr/abims/
On 05/12/2010 09:53 AM, Loraine Brillet wrote:
thanks!
Could you please give me the url for this web page, I can't find it.
see: http://bitbucket.org/galaxy/galaxy-central/wiki/ThirdPartyTools
Loraine
James Taylor wrote:
We're working on such a place where users can share their tools (and workflows), and the community can provide feedback.
In the meantime, we recommend using the "ThirdPartyTools" page on the galaxy wiki.
On May 7, 2010, at 5:02 AM, Loraine Brillet wrote:
Is there any data warehouse where xml program description for galaxy are left and shared ?
Hello Loraine, The ThirdPartyTools wiki is at http://bitbucket.org/galaxy/galaxy-central/wiki/ThirdPartyTools To easily find any of our wiki pages, visit our site map at http://bitbucket.org/galaxy/galaxy-central/wiki/SiteMap Thanks! On May 12, 2010, at 3:53 AM, Loraine Brillet wrote:
thanks!
Could you please give me the url for this web page, I can't find it.
Loraine
James Taylor wrote:
We're working on such a place where users can share their tools (and workflows), and the community can provide feedback.
In the meantime, we recommend using the "ThirdPartyTools" page on the galaxy wiki.
On May 7, 2010, at 5:02 AM, Loraine Brillet wrote:
Is there any data warehouse where xml program description for galaxy are left and shared ?
-- Loraine Brillet
Service Informatique et Genomique Plateforme ABiMS (Analyses and Bioinformatics for Marine Sciences) Station Biologique de Roscoff FR 2424 CNRS UPMC Place Georges Teissier 29682 Roscoff Cedex tel: ++33 (0)2 98 29 25 50 fax: ++33 (0)2 98 29 23 24 email: loraine.brillet@sb-roscoff.fr http://www.sb-roscoff.fr http://www.sb-roscoff.fr/abims/
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Greg Von Kuster Galaxy Development Team greg@bx.psu.edu
Hi, On May 7, 2010, at 3:20 PM, James Taylor wrote:
We're working on such a place where users can share their tools (and workflows), and the community can provide feedback.
A place to share tool configs (and tools) would be great! I have some to share and I know others in NBIC have some too.... As for sharing / publishing workflows and community feedback I would suggest to take a serious look at myExperiment (http://www.myexperiment.org/) as that already handles more or less everything you would need and I'm sure you don't want to reinvent the square wheel :o. Galaxy could be added as a "known" workflow system as per http://wiki.myexperiment.org/index.php/Workflow_systems ... Cheers, Pi
In the meantime, we recommend using the "ThirdPartyTools" page on the galaxy wiki.
On May 7, 2010, at 5:02 AM, Loraine Brillet wrote:
Is there any data warehouse where xml program description for galaxy are left and shared ?
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participants (8)
-
Greg Von Kuster -
Hans-Rudolf Hotz -
James Taylor -
Jeremy Goecks -
Jeremy Goecks -
Loraine Brillet -
Pieter Neerincx -
SHAUN WEBB