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


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