On Thu, Mar 7, 2013 at 8:21 AM, Adam Cohn <span dir="ltr">&lt;<a href="mailto:adamcohn@genepeeks.com" target="_blank">adamcohn@genepeeks.com</a>&gt;</span> wrote:<br><div class="gmail_quote"><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">

<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>Hi Galaxy Admin list, </div><div><br></div><div>This is my first post to this list.  Galaxy is a great tool and I am really enjoying working with it. </div>

<div><br></div><div>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&#39;t find the answers.  Thanks in advance for your help.</div>

<div><br></div><div><b>Question 1: Can&#39;t install tools in the tool shed</b></div><div><br></div><div>I have added this line to the universe_wsgi.ini</div><div><br></div><div>tool_config_file = tool_conf.xml,shed_tool_conf.xml</div>

<div><br></div><div>Which references a file that contains this tag:</div><div><br></div><div><div>&lt;toolbox tool_path=&quot;../shed_tools&quot;&gt;</div><div>&lt;/toolbox&gt;</div></div><div><br></div><div>I have created this directory at the correct level and set permission to 755.</div>

<div><br></div><div>But I am still getting a non specific error loading tools.  </div><div>I saw that this was (is?) a known issue, but that it had been resolved in the latest build. What am I missing?</div><div>The log does not give me any more specific information about the error.</div>

<div><br></div><div>Any suggestions?</div></div></blockquote><div><br></div><div><br></div><div>Can you give any more information about the error you&#39;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.</div>

<div><br></div><div>Additionally, because of where the shed tools are currently installed, you&#39;ll also need to &#39;persist galaxyTools&#39; in the cloud admin interface once you have your instance how you want it.</div>

<div><br></div><div>It&#39;s worth mentioning that there&#39;s a new cloud release pending, currently being tested, that will streamline this process.</div><div><br></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">

<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div><b>Question 2:  Weird log error.</b></div><div> Every minute the log records this error:</div><div><pre style="color:rgb(48,48,48);font-size:10px">
galaxy.web.framework DEBUG 2013-03-07 13:07:42,207 Error: this request returned None from get_history(): <a href="http://127.0.0.1:8080/root" target="_blank">http://127.0.0.1:8080/root</a>
127.0.0.1 - - [07/Mar/2013:13:07:42 +0000] &quot;GET /root HTTP/1.1&quot; 200 - &quot;-&quot; &quot;Python-urllib/2.6&quot;</pre></div><div>Is this a known issue?  How can I find more information about what is causing it?</div>

</div></blockquote><div><br></div><div><br></div><div>Safe to ignore this.</div><div> </div><div><br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div><div><b>Question 3:  </b><b>Correct Settings</b>:  My intent is to allow employees to access galaxy remotely without allowing public access.  In order to keep the data private, I have set:</div>

<div><br></div><div>require_login = True</div><div>allow_user_creation = False</div><div><br></div><div>Other than the id_secret setting (which I am currently researching) are there any big security holes I am missing with the default installation?</div>

</div><div><span style="font-family:arial;font-size:small"></span></div></div></blockquote><div><br></div><div><br></div><div>I&#39;m interested to see what other people suggest here, but it&#39;s a start.  For this use case, I&#39;d probably recommend setting up external authentication (instead of require_login using galaxy&#39;s auth) integrated with nginx on the cloud instance -- see more information about this here: <a href="http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy">http://wiki.galaxyproject.org/Admin/Config/Performance/nginx%20Proxy</a></div>
<div><br></div><div>-Dannon</div></div>