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
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 kusalik@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/
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 kusalik@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/
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 dave@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 kusalik@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/
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 kusalik@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 dave@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 kusalik@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/
galaxy-dev@lists.galaxyproject.org
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Dave Bouvier -
David Hoover -
Greg Von Kuster -
Tony Kusalik