On Thu, Mar 7, 2013 at 8:21 AM, Adam Cohn <adamc...@genepeeks.com> wrote:

> Hi Galaxy Admin list,
>
> This is my first post to this list.  Galaxy is a great tool and I am
> really enjoying working with it.
>
> Background, I am setting up a private galaxy instance for my company using
> AWS.  The installation is going very smoothly with a few problems listed
> below. I apologize if these questions have been asked before.  I have been
> through the documentation and searched the list pretty thoroughly and can't
> find the answers.  Thanks in advance for your help.
>
> *Question 1: Can't install tools in the tool shed*
>
> I have added this line to the universe_wsgi.ini
>
> tool_config_file = tool_conf.xml,shed_tool_conf.xml
>
> Which references a file that contains this tag:
>
> <toolbox tool_path="../shed_tools">
> </toolbox>
>
> I have created this directory at the correct level and set permission to
> 755.
>
> But I am still getting a non specific error loading tools.
> I saw that this was (is?) a known issue, but that it had been resolved in
> the latest build. What am I missing?
> The log does not give me any more specific information about the error.
>
> Any suggestions?
>


Can you give any more information about the error you're seeing?  The only
step necessary to install tools out of the toolshed should be to uncomment
the single line referencing shed_tool_conf.xml from your universe_wsgi.ini.
 The creation of the shed_tools directory, etc., should all be automatic
beyond that point.

Additionally, because of where the shed tools are currently installed,
you'll also need to 'persist galaxyTools' in the cloud admin interface once
you have your instance how you want it.

It's worth mentioning that there's a new cloud release pending, currently
being tested, that will streamline this process.



> *Question 2:  Weird log error.*
>  Every minute the log records this error:
>
> galaxy.web.framework DEBUG 2013-03-07 13:07:42,207 Error: this request 
> returned None from get_history(): http://127.0.0.1:8080/root
> 127.0.0.1 - - [07/Mar/2013:13:07:42 +0000] "GET /root HTTP/1.1" 200 - "-" 
> "Python-urllib/2.6"
>
> Is this a known issue?  How can I find more information about what is
> causing it?
>


Safe to ignore this.


*Question 3:  **Correct Settings*:  My intent is to allow employees to
> access galaxy remotely without allowing public access.  In order to keep
> the data private, I have set:
>
> require_login = True
> allow_user_creation = False
>
> Other than the id_secret setting (which I am currently researching) are
> there any big security holes I am missing with the default installation?
>


I'm interested to see what other people suggest here, but it's a start.
 For this use case, I'd probably recommend setting up external
authentication (instead of require_login using galaxy's auth) integrated
with nginx on the cloud instance -- see more information about this here:
http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy

-Dannon
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