Hello,

I have a created an answer for this question in the planemo tool
development tutorial:

http://planemo.readthedocs.org/en/latest/writing_standalone.html#determined-the-user-submitting-a-job

From the docs:

The variable ``$__user_email__`` (as well as ``$__user_name__`` and
``$__user_id__``) is available when building up your command in
the tool's ``<command>`` block. The following tool demonstrates the use of
this and a few other special parameters available to all tools.

- `special_params.xml
<https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/special_params.xml>`__

Hope this helps,
-John


On Wed, Apr 15, 2015 at 8:51 AM, Wang, Yu <yu.w...@lrz.de> wrote:
> Hi,
>
> Is there a way to query the actual name of the user, who is logged into
> galaxy and submitted the workflow ($REMOTE_USER),  from inside a galaxy tool
>
> when galaxy is configured for external authentication using an apache
> server?
>
>
> It seems like galaxy passes this variable to scripts like
> 'drmaa_external_runner.py' but I could not find it in the environment of a
> tool
>
> which has been started via e.g. python ( using  <command
> interpreter="python"> in the xml-file of the tool)."
>
>
> Cheers,
> Yu
>
> di29her
> w...@lrz.de
>
> On 13 Apr 2015, at 18:00, galaxy-dev-requ...@lists.galaxyproject.org wrote:
>
> Send galaxy-dev mailing list submissions to
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> Today's Topics:
>
>   1. Re: Strange repository dependency behavior with
>      toolshed-installed naive_variant_caller (Martin Čech)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 13 Apr 2015 14:27:10 +0000
> From: Martin Čech <mar...@bx.psu.edu>
> To: Brian Claywell <bclay...@fredhutch.org>
> Cc: galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] Strange repository dependency behavior with
> toolshed-installed naive_variant_caller
> Message-ID:
> <cahkbqufw66cxyss7kjexm4-mpdk0p_tlt_xtcobek4pls3o...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> 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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