Hello Brian,

we have made some changes in the past month that might address the issue
you are having. Are you still encountering problems? If so could you please
try re-installing the tools again?

thank you

Martin

On Tue, Feb 24, 2015 at 5:15 PM Brian Claywell <bclay...@fredhutch.org>
wrote:

> 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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