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
>>> 
>>> 
>>> ___________________________________________________________
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>> 
>> 
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