Dannon,
Thanks for the quick response.

I tried to install a tool from the galaxy test too shed and received the
following information, though I am not sure what will be useful to you.  I
will definitely keep my eye out for the new release and will check into the
authentication method you suggested.

URL: 
http://testtoolshed.g2.bx.psu.edu/repository/install_repositories_by_revisio
n?changeset_revisions=1d2730e6bb39&repository_ids=5483924c34f005f2
Module paste.exceptions.errormiddleware:144 in __call__
>>   
<http://testtoolshed.g2.bx.psu.edu/repository/install_repositories_by_revision?c
hangeset_revisions=1d2730e6bb39&repository_ids=5483924c34f005f2#> app_iter =
self.application(environ, sr_checker)
Module paste.debug.prints:106 in __call__
>>   
<http://testtoolshed.g2.bx.psu.edu/repository/install_repositories_by_revision?c
hangeset_revisions=1d2730e6bb39&repository_ids=5483924c34f005f2#> environ,
self.app)
Module paste.wsgilib:543 in intercept_output
>>   
<http://testtoolshed.g2.bx.psu.edu/repository/install_repositories_by_revision?c
hangeset_revisions=1d2730e6bb39&repository_ids=5483924c34f005f2#> app_iter =
application(environ, replacement_start_response)
Module paste.recursive:84 in __call__
>>   
<http://testtoolshed.g2.bx.psu.edu/repository/install_repositories_by_revision?c
hangeset_revisions=1d2730e6bb39&repository_ids=5483924c34f005f2#> return
self.application(environ, start_response)
Module paste.httpexceptions:633 in __call__
>>   
<http://testtoolshed.g2.bx.psu.edu/repository/install_repositories_by_revision?c
hangeset_revisions=1d2730e6bb39&repository_ids=5483924c34f005f2#> return
self.application(environ, start_response)
Module galaxy.web.framework.base:128 in __call__
>>   
<http://testtoolshed.g2.bx.psu.edu/repository/install_repositories_by_revision?c
hangeset_revisions=1d2730e6bb39&repository_ids=5483924c34f005f2#> return
self.handle_request( environ, start_response )
Module galaxy.web.framework.base:184 in handle_request
>>   
<http://testtoolshed.g2.bx.psu.edu/repository/install_repositories_by_revision?c
hangeset_revisions=1d2730e6bb39&repository_ids=5483924c34f005f2#> body = method(
trans, **kwargs )
Module galaxy.webapps.tool_shed.controllers.repository:1439 in
install_repositories_by_revision
>>   
<http://testtoolshed.g2.bx.psu.edu/repository/install_repositories_by_revision?c
hangeset_revisions=1d2730e6bb39&repository_ids=5483924c34f005f2#> ( web.url_for(
'/', qualified=True ), ','.join( util.listify( repository_ids ) ), ','.join(
util.listify( changeset_revisions ) ) ) )
Module tool_shed.util.shed_util_common:4029 in url_join
>>   
<http://testtoolshed.g2.bx.psu.edu/repository/install_repositories_by_revision?c
hangeset_revisions=1d2730e6bb39&repository_ids=5483924c34f005f2#> parts.append(
arg.strip( '/' ) )
AttributeError: 'NoneType' object has no attribute 'strip'

CGI Variables
CONTENT_LENGTH'0'
HTTP_ACCEPT'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8'
HTTP_ACCEPT_ENCODING'gzip, deflate'
HTTP_ACCEPT_LANGUAGE'en-us'
HTTP_CONNECTION'close'
HTTP_DNT'1'
HTTP_HOST'testtoolshed.g2.bx.psu.edu'
HTTP_REFERER'http://testtoolshed.g2.bx.psu.edu/repository/preview_tools_in_c
hangeset?repository_id=5483924c34f005f2&changeset_revision=1d2730e6bb39'
HTTP_USER_AGENT'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2)
AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 Safari/536.26.17'
HTTP_X_FORWARDED_FOR'76.100.61.154'
HTTP_X_FORWARDED_HOST'testtoolshed.g2.bx.psu.edu'
ORGINAL_HTTP_HOST'testtoolshed_app'
ORGINAL_REMOTE_ADDR'127.0.0.1'
PATH_INFO'/repository/install_repositories_by_revision'
QUERY_STRING'changeset_revisions=1d2730e6bb39&repository_ids=5483924c34f005f
2'
REMOTE_ADDR'76.100.61.154'
REQUEST_METHOD'GET'
SERVER_NAME'127.0.0.1'
SERVER_PORT'9930'
SERVER_PROTOCOL'HTTP/1.0'
WSGI Variables
application<paste.debug.prints.PrintDebugMiddleware object at 0x6855910>
paste.cookies(<SimpleCookie: >, '')
paste.expected_exceptions[<class 'paste.httpexceptions.HTTPException'>]
paste.httpexceptions<paste.httpexceptions.HTTPExceptionHandler object at
0x6843f90>
paste.httpserver.thread_pool<paste.httpserver.ThreadPool object at
0x6a0ccd0>
paste.parsed_querystring([('changeset_revisions', '1d2730e6bb39'),
('repository_ids', '5483924c34f005f2')],
'changeset_revisions=1d2730e6bb39&repository_ids=5483924c34f005f2')
paste.printdebug_listeners[<cStringIO.StringO object at 0x87178f0>,
<galaxy.util.pastescript.serve.LazyWriter object at 0x31694d0>]
paste.recursive.forward<paste.recursive.Forwarder from />
paste.recursive.include<paste.recursive.Includer from />
paste.recursive.include_app_iter<paste.recursive.IncluderAppIter from />
paste.recursive.script_name''
paste.remove_printdebug<function remove_printdebug at 0x5868758>
paste.throw_errorsTrue
webob._parsed_query_vars(MultiDict([('changeset_revisions', '1d2730e6bb39'),
('repository_ids', '5483924c34f005f2')]),
'changeset_revisions=1d2730e6bb39&repository_ids=5483924c34f005f2')
wsgi process'Multithreaded'

From:  Dannon Baker <dannon.ba...@gmail.com>
Date:  Thursday, March 7, 2013 9:03 AM
To:  Adam Cohn <adamc...@genepeeks.com>
Cc:  <galaxy-dev@lists.bx.psu.edu>
Subject:  Re: [galaxy-dev] Some problems setting up a new cloudman instance
on AWS

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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