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
``$__user_id__``) is available when building up your command in
the tool's ``<command>`` block. The following tool demonstrates the use of
this and a few other special parameters available to all tools.
- `special_params.xml
<https://github.com/galaxyproject/galaxy/blob/dev/test/functional/tools/special_params.xml>`__
Hope this helps,
-John
On Wed, Apr 15, 2015 at 8:51 AM, Wang, Yu <Yu.Wang@lrz.de> wrote:
Hi,
Is there a way to query the actual name of the user, who is logged into
galaxy and submitted the workflow ($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
wang@lrz.de
On 13 Apr 2015, at 18:00, galaxy-dev-request@lists.galaxyproject.org wrote:
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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 <marten@bx.psu.edu>
To: Brian Claywell <bclaywel@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_xtCOBEK4pLs3OYOg@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 <bclaywel@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 <marten@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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