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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