Re: [galaxy-dev] problem with bioc_qvalue, Version: 1.34.0
David, Tony, I have not yet been able to reproduce the behavior you've reported here. I will continue to investigate, but if you go to Manage installed tool shed repositories in your Galaxy admin interface and select the Update tool shed status option on the compute_q_values repository, your Galaxy instance should detect that there is an update available and give you the option to update the repository and install its dependencies. Your report did help me uncover a potentially related issue with determining dependencies of repositories that have been updated after being added to the migrate_tools definition, which has now been resolved. --Dave B. On 04/17/2014 04:35 PM, David Hoover wrote: I saw the same phenomenon. I think it stems from the current version of compute_q_values pointing to unavailable revisions of both R and the bioc_qvalue R package. Whoever maintains the compute_q_values needs to straighten out the revision ids. David Hoover Helix Systems Staff National Institutes of Health On Apr 17, 2014, at 1:38 PM, Tony Kusalik kusa...@cs.usask.ca wrote: Hi, I am having a problem with updating our local Galaxy server, and I am hoping someone can help me. Yesterday I performed a 'hg incoming' command. A bunch of updates were applied, from changeset 12443:ec9d31a8bc04 to changeset 13068:c05752549163. I restarted the server (in daemon mode), but it halted. The content of paster.log instructed me to run sh ./scripts/migrate_tools/0010_tools.sh I did that. That script encountered an error: The following error occurred from the InstallManager while installing tool dependency bioc_qvalue : Error installing tool dependency package bioc_qvalue version 1.34.0: Unable to locate required tool shed repository named package_bioc_qvalue_1_34_0 owned by devteam with revision 11735242a19e. How do I get around this problem? I checked the mailing lists for anyone reporting a problem with bioc_qvalue or 11735242a19e but nothing was turned up. Tony Kusalik ___ 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/ ___ 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] problem with bioc_qvalue, Version: 1.34.0
Thanks for the response. I have made some progress, but I don't seem to be out-of-the-woods yet. I realized that when I had invoked sh ./scripts/migrate_tools/0010_tools.sh I had done it as root, rather than as user galaxy. Hence I did a chmod -R galaxy:galaxy on both the shed_tools/ and tool_dependencies/ directories. Then in the Galaxy Admin interface I selected the Installed tool shed repositories option. I clicked on update tool shed status in the upper right corner. I waited for that update to complete. About 15 lines down the window is the line for compute_q_values. It's installation status was given as Installed, missing tool dependencies. At the very left, it was marked with a green check mark (This is the latest installable revision of this repository) and an attention symbol (Updates are available in the Tool Shed for this revision). I choose get updates from the pull-down menu associated with compute_q_values. The update window appeared, and I toggled on Install. The installation SEEMED to be okay. Now I went back to the Installed tool shed repositories window. compute_q_values was marked with just a green check mark. The revision column/field is given as 62f7b9c20c9b. The only problem is that the Installation Status is still marked with Installed, missing tool dependencies. Looking at the last 100 or so lines of paster.log, it appears that the install of compute_q_values was indeed successful. Nothing about missing dependencies reported there. Selecting update tool shed status does not change anything. Suggestions? Should I try running sh ./scripts/migrate_tools/0010_tools.sh again? Or might that just make matters worse? On 2014-04-22, at 7:56 , Dave Bouvier d...@bx.psu.edu wrote: David, Tony, I have not yet been able to reproduce the behavior you've reported here. I will continue to investigate, but if you go to Manage installed tool shed repositories in your Galaxy admin interface and select the Update tool shed status option on the compute_q_values repository, your Galaxy instance should detect that there is an update available and give you the option to update the repository and install its dependencies. Your report did help me uncover a potentially related issue with determining dependencies of repositories that have been updated after being added to the migrate_tools definition, which has now been resolved. --Dave B. On 04/17/2014 04:35 PM, David Hoover wrote: I saw the same phenomenon. I think it stems from the current version of compute_q_values pointing to unavailable revisions of both R and the bioc_qvalue R package. Whoever maintains the compute_q_values needs to straighten out the revision ids. David Hoover Helix Systems Staff National Institutes of Health On Apr 17, 2014, at 1:38 PM, Tony Kusalik kusa...@cs.usask.ca wrote: Hi, I am having a problem with updating our local Galaxy server, and I am hoping someone can help me. Yesterday I performed a 'hg incoming' command. A bunch of updates were applied, from changeset 12443:ec9d31a8bc04 to changeset 13068:c05752549163. I restarted the server (in daemon mode), but it halted. The content of paster.log instructed me to run sh ./scripts/migrate_tools/0010_tools.sh I did that. That script encountered an error: The following error occurred from the InstallManager while installing tool dependency bioc_qvalue : Error installing tool dependency package bioc_qvalue version 1.34.0: Unable to locate required tool shed repository named package_bioc_qvalue_1_34_0 owned by devteam with revision 11735242a19e. How do I get around this problem? I checked the mailing lists for anyone reporting a problem with bioc_qvalue or 11735242a19e but nothing was turned up. Tony Kusalik ___ 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/ ___ 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] problem with bioc_qvalue, Version: 1.34.0
Hi Tony, It may be easiest to just uninstall / reinstall the repository from the Manage installed tool shed repositories option in the admin menu. Greg Von Kuster On Apr 22, 2014, at 4:21 PM, Tony Kusalik kusa...@cs.usask.ca wrote: Thanks for the response. I have made some progress, but I don't seem to be out-of-the-woods yet. I realized that when I had invoked sh ./scripts/migrate_tools/0010_tools.sh I had done it as root, rather than as user galaxy. Hence I did a chmod -R galaxy:galaxy on both the shed_tools/ and tool_dependencies/ directories. Then in the Galaxy Admin interface I selected the Installed tool shed repositories option. I clicked on update tool shed status in the upper right corner. I waited for that update to complete. About 15 lines down the window is the line for compute_q_values. It's installation status was given as Installed, missing tool dependencies. At the very left, it was marked with a green check mark (This is the latest installable revision of this repository) and an attention symbol (Updates are available in the Tool Shed for this revision). I choose get updates from the pull-down menu associated with compute_q_values. The update window appeared, and I toggled on Install. The installation SEEMED to be okay. Now I went back to the Installed tool shed repositories window. compute_q_values was marked with just a green check mark. The revision column/field is given as 62f7b9c20c9b. The only problem is that the Installation Status is still marked with Installed, missing tool dependencies. Looking at the last 100 or so lines of paster.log, it appears that the install of compute_q_values was indeed successful. Nothing about missing dependencies reported there. Selecting update tool shed status does not change anything. Suggestions? Should I try running sh ./scripts/migrate_tools/0010_tools.sh again? Or might that just make matters worse? On 2014-04-22, at 7:56 , Dave Bouvier d...@bx.psu.edu wrote: David, Tony, I have not yet been able to reproduce the behavior you've reported here. I will continue to investigate, but if you go to Manage installed tool shed repositories in your Galaxy admin interface and select the Update tool shed status option on the compute_q_values repository, your Galaxy instance should detect that there is an update available and give you the option to update the repository and install its dependencies. Your report did help me uncover a potentially related issue with determining dependencies of repositories that have been updated after being added to the migrate_tools definition, which has now been resolved. --Dave B. On 04/17/2014 04:35 PM, David Hoover wrote: I saw the same phenomenon. I think it stems from the current version of compute_q_values pointing to unavailable revisions of both R and the bioc_qvalue R package. Whoever maintains the compute_q_values needs to straighten out the revision ids. David Hoover Helix Systems Staff National Institutes of Health On Apr 17, 2014, at 1:38 PM, Tony Kusalik kusa...@cs.usask.ca wrote: Hi, I am having a problem with updating our local Galaxy server, and I am hoping someone can help me. Yesterday I performed a 'hg incoming' command. A bunch of updates were applied, from changeset 12443:ec9d31a8bc04 to changeset 13068:c05752549163. I restarted the server (in daemon mode), but it halted. The content of paster.log instructed me to run sh ./scripts/migrate_tools/0010_tools.sh I did that. That script encountered an error: The following error occurred from the InstallManager while installing tool dependency bioc_qvalue : Error installing tool dependency package bioc_qvalue version 1.34.0: Unable to locate required tool shed repository named package_bioc_qvalue_1_34_0 owned by devteam with revision 11735242a19e. How do I get around this problem? I checked the mailing lists for anyone reporting a problem with bioc_qvalue or 11735242a19e but nothing was turned up. Tony Kusalik ___ 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/ ___ Please keep all replies on the list by using reply all in your mail client.
Re: [galaxy-dev] problem with bioc_qvalue, Version: 1.34.0
I saw the same phenomenon. I think it stems from the current version of compute_q_values pointing to unavailable revisions of both R and the bioc_qvalue R package. Whoever maintains the compute_q_values needs to straighten out the revision ids. David Hoover Helix Systems Staff National Institutes of Health On Apr 17, 2014, at 1:38 PM, Tony Kusalik kusa...@cs.usask.ca wrote: Hi, I am having a problem with updating our local Galaxy server, and I am hoping someone can help me. Yesterday I performed a 'hg incoming' command. A bunch of updates were applied, from changeset 12443:ec9d31a8bc04 to changeset 13068:c05752549163. I restarted the server (in daemon mode), but it halted. The content of paster.log instructed me to run sh ./scripts/migrate_tools/0010_tools.sh I did that. That script encountered an error: The following error occurred from the InstallManager while installing tool dependency bioc_qvalue : Error installing tool dependency package bioc_qvalue version 1.34.0: Unable to locate required tool shed repository named package_bioc_qvalue_1_34_0 owned by devteam with revision 11735242a19e. How do I get around this problem? I checked the mailing lists for anyone reporting a problem with bioc_qvalue or 11735242a19e but nothing was turned up. Tony Kusalik ___ 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/
