Hi Martin,

Thanks for the prompt reply! My responses are inline below.

On Tue, Feb 24, 2015 at 8:26 AM, Martin Čech <mar...@bx.psu.edu> wrote:

> Are you using Admin UI for installation or API scripts?
>

The admin UI exclusively.


> Does the 'installed tool shed repos' page show multiple installations of
> the same package (with the same changesets)? If so what are the states of
> these?
>

Yes -- the iuc package_numpy_1_7 revision a4bdc17eed4a is listed twice,
with both showing the green "Installed" status. Interestingly the installed
repo page shows that they're installed in different locations:

(...)/shed_tools/
toolshed.g2.bx.psu.edu/repos/iuc/package_numpy_1_7/ef12a3a11d5b/package_numpy_1_7
(...)/shed_tools/
toolshed.g2.bx.psu.edu/repos/iuc/package_numpy_1_7/a4bdc17eed4a/package_numpy_1_7

At one point during the troubleshooting steps I described in my original
email, package_pybamparser_0_0_1 and package_pybamtools_0_0_1 showed up in
the same way, with two records each having the same revision and a green
"Installed" status.

If you check on the filesystem in the
> {{configured_dependency_dir}}/path/to/duplicated/package do you see any
> strange stuff/duplication?
>

I didn't see anything that struck me as out of the ordinary. Here's a gist
of the directory structures for the affected packages under both shed_tools
and tool_deps:

https://gist.github.com/bcclaywell/23c0b274f2d4bd0d659f

How big is your Galaxy in terms of installed tools, complexity of setup and
> traffic?
>

I don't think it's terribly big -- we have a couple of large tool suites
like BEDTools, the gops interval operations suites, GATK 1 and 2, etc, and
then maybe 15-20 other tools and their dependencies?

Our setup isn't very complex, either; Galaxy is running with one web
process and one handler process behind an nginx reverse proxy, all running
on a single machine. Jobs are submitted to our slurm cluster via the SSH
CLI runner.

Traffic is pretty low -- we're just now rolling out of beta.


Cheers,

Brian

-- 
Brian Claywell | programmer/analyst
Matsen Group   | http://matsen.fredhutch.org <http://matsen.fhcrc.org/>
Fred Hutchinson Cancer Research Center
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