Re: [galaxy-dev] import Workflow from public Galaxy to local instance
Andreas, export your history to tgz. then locally import it. I have to say that we do this for backup purposesbut it is a pain.exporting takes sometimes ages even for small histories. I am not sure how well synced your databases and such should be.(unique identifiers and such). Never tested that... Alex Van: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] namens Andreas Kuntzagk [andreas.kuntz...@mdc-berlin.de] Verzonden: dinsdag 21 mei 2013 17:56 To: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] import Workflow from public Galaxy to local instance Hi, I want to make workflows published on usegalaxy.org available for users on our local instance. How do I do this? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] import Workflow from public Galaxy to local instance
I tracked down this issue to a bug in the workflow export code, and I've fixed it. The fix will appear on our public server early next week; please let us know if you're still seeing this error late next week. Best, J. On May 23, 2013, at 9:50 AM, Andreas Kuntzagk wrote: For the first of the CloudMap workflows that worked. But the second failes with this error message: Failed to open URL: https://main.g2.bx.psu.edu/workflow/export_to_file?id=f444ce954bdc4953 Exception: HTTP Error 500: Internal Server Error I don't see any information in the log files. regards, Andreas On 22.05.2013 13:57, Dannon Baker wrote: On Wed, May 22, 2013 at 3:12 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de mailto:andreas.kuntz...@mdc-berlin.de wrote: But how do I get the workflow_id? For example for the workflow https://main.g2.bx.psu.edu/u/__gm2123/w/cloudmap-unmapped-__mutant-workflow-no-candidates https://main.g2.bx.psu.edu/u/gm2123/w/cloudmap-unmapped-mutant-workflow-no-candidates what would the workflow_id be? (I tried cloudmap-unmapped-mutant-__workflow-no-candidates but this did not work.) If you click on that link above, you can see the id in the url for the 'Import' link. Again, definitely not optimal -- public workflows should probably all be exposed via the API for use/import. -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] import Workflow from public Galaxy to local instance
For the first of the CloudMap workflows that worked. But the second failes with this error message: Failed to open URL: https://main.g2.bx.psu.edu/workflow/export_to_file?id=f444ce954bdc4953 Exception: HTTP Error 500: Internal Server Error I don't see any information in the log files. regards, Andreas On 22.05.2013 13:57, Dannon Baker wrote: On Wed, May 22, 2013 at 3:12 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de mailto:andreas.kuntz...@mdc-berlin.de wrote: But how do I get the workflow_id? For example for the workflow https://main.g2.bx.psu.edu/u/__gm2123/w/cloudmap-unmapped-__mutant-workflow-no-candidates https://main.g2.bx.psu.edu/u/gm2123/w/cloudmap-unmapped-mutant-workflow-no-candidates what would the workflow_id be? (I tried cloudmap-unmapped-mutant-__workflow-no-candidates but this did not work.) If you click on that link above, you can see the id in the url for the 'Import' link. Again, definitely not optimal -- public workflows should probably all be exposed via the API for use/import. -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] import Workflow from public Galaxy to local instance
Hi, On 21.05.2013 18:06, Dannon Baker wrote: This interaction is pretty clunky right now (I've made a trello card for improving it: https://trello.com/c/eu8XiJLK. Two options right now are: 1) Import (on main) each workflow you want to copy to your local instance, and generate the regular download link for import. (Download or Export in the workflow menu, once you've imported it) I wanted to avoid that since I have to import more then one workflow. 2) Munge the URLs yourself -- all accessible workflows are available for download via https://main.g2.bx.psu.edu/workflow/export_to_file?id=workflow_id But how do I get the workflow_id? For example for the workflow https://main.g2.bx.psu.edu/u/gm2123/w/cloudmap-unmapped-mutant-workflow-no-candidates what would the workflow_id be? (I tried cloudmap-unmapped-mutant-workflow-no-candidates but this did not work.) regards, Andreas -Dannon On Tue, May 21, 2013 at 11:56 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de mailto:andreas.kuntz...@mdc-berlin.de wrote: Hi, I want to make workflows published on usegalaxy.org http://usegalaxy.org available for users on our local instance. How do I do this? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/__bimsb/BIMSB_groups/Dieterich http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich _ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/__search/mailinglists/ http://galaxyproject.org/search/mailinglists/ -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] import Workflow from public Galaxy to local instance
On Wed, May 22, 2013 at 3:12 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de wrote: But how do I get the workflow_id? For example for the workflow https://main.g2.bx.psu.edu/u/**gm2123/w/cloudmap-unmapped-** mutant-workflow-no-candidateshttps://main.g2.bx.psu.edu/u/gm2123/w/cloudmap-unmapped-mutant-workflow-no-candidates what would the workflow_id be? (I tried cloudmap-unmapped-mutant-**workflow-no-candidates but this did not work.) If you click on that link above, you can see the id in the url for the 'Import' link. Again, definitely not optimal -- public workflows should probably all be exposed via the API for use/import. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] import Workflow from public Galaxy to local instance
Hi, I want to make workflows published on usegalaxy.org available for users on our local instance. How do I do this? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] import Workflow from public Galaxy to local instance
This interaction is pretty clunky right now (I've made a trello card for improving it: https://trello.com/c/eu8XiJLK. Two options right now are: 1) Import (on main) each workflow you want to copy to your local instance, and generate the regular download link for import. (Download or Export in the workflow menu, once you've imported it) 2) Munge the URLs yourself -- all accessible workflows are available for download via https://main.g2.bx.psu.edu/workflow/export_to_file?id= workflow_id -Dannon On Tue, May 21, 2013 at 11:56 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de wrote: Hi, I want to make workflows published on usegalaxy.org available for users on our local instance. How do I do this? regards, Andreas -- Andreas Kuntzagk SystemAdministrator Berlin Institute for Medical Systems Biology at the Max-Delbrueck-Center for Molecular Medicine Robert-Roessle-Str. 10, 13125 Berlin, Germany http://www.mdc-berlin.de/en/**bimsb/BIMSB_groups/Dieterichhttp://www.mdc-berlin.de/en/bimsb/BIMSB_groups/Dieterich __**_ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/**search/mailinglists/http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
