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)."



On 13 Apr 2015, at 18:00, 

Send galaxy-dev mailing list submissions to

To subscribe or unsubscribe via the World Wide Web, visit
or, via email, send a message with subject or body 'help' to

You can reach the person managing the list at

When replying, please edit your Subject line so it is more specific
than "Re: Contents of galaxy-dev digest..."

HEY!  This is important!  If you reply to a thread in a digest, please
1. Change the subject of your response from "Galaxy-dev Digest Vol ..." to the 
original subject for the thread.
2. Strip out everything else in the digest that is not part of the thread you 
are responding to.

1. This will keep the subject meaningful.  People will have some idea from the 
subject line if they should read it or not.
2. Not doing this greatly increases the number of emails that match search 
queries, but that aren't actually informative.

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
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


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

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

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:


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:


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.



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

-------------- next part --------------
An HTML attachment was scrubbed...


Subject: Digest Footer

galaxy-dev mailing list

To search Galaxy mailing lists use the unified search at:


End of galaxy-dev Digest, Vol 106, Issue 12

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:

Reply via email to