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(a)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
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
I clicked on "update tool shed status" in the upper right corner. I waited for
that update to
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
that the "Installation Status" is still marked with "Installed, missing
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
Selecting "update tool shed status" does not change anything.
Suggestions? Should I try running
again? Or might that just make matters worse?
On 2014-04-22, at 7:56 , Dave Bouvier <dave(a)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
>> David Hoover
>> Helix Systems Staff
>> National Institutes of Health
>> On Apr 17, 2014, at 1:38 PM, Tony Kusalik <kusalik(a)cs.usask.ca> wrote:
>>> 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"
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>> 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:
>> To search Galaxy mailing lists use the unified search at:
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:
To search Galaxy mailing lists use the unified search at: