Difference between revisions of "Design Specs: GBrowse Integration"

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1. use the front proxy (nginx) to pass requests from /gb2 to the gbrowse server.
+
= Proxy configuration =
 +
 
 +
use the front proxy (nginx) to pass requests from /gb2 to the gbrowse server
 +
 
 
On dev, I have  
 
On dev, I have  
 
  <pre>
 
  <pre>
Line 14: Line 17:
 
  </pre>
 
  </pre>
  
2. copy over the head header footer stanza in conf/gbrowse.conf/GBrowse.conf
+
= GBrowse Configuration =
 +
== header & footer ==
 +
copy over the head header footer stanza in conf/gbrowse.conf/GBrowse.conf
  
 
Note: things might change in future as we change the header.
 
Note: things might change in future as we change the header.
Line 56: Line 61:
  
 
</pre>
 
</pre>
3. add stylesheet  = /css/wormbase-gbrowse.css
+
 
 +
= CSS =
 +
 +
add stylesheet  = /css/wormbase-gbrowse.css
  
 
This is needed for some css conflict between WormBase & GBrowse
 
This is needed for some css conflict between WormBase & GBrowse
 +
 +
= URL change within APP itself =
 +
 +
go into root/templates/config/external_urls
 +
<pre>
 +
  [% site.external_urls = {
 +
genomic_location = { description  = 'The WormBase Genome Browser'
 +
      maintainer  = ''
 +
      base        = '/gb2/gbrowse/'
 +
      search      = '/gb2/gbrowse/%s' 
 +
    }
 +
 +
gbrowse_image = { description  = 'The WormBase Genome Browser Image'
 +
      maintainer  = ''
 +
      base        = '/gb2/gbrowse_img/'
 +
      search      = '/gb2/gbrowse_img/%s' 
 +
    }
 +
  ...
 +
</pre>

Latest revision as of 20:30, 27 January 2011

Proxy configuration

use the front proxy (nginx) to pass requests from /gb2 to the gbrowse server

On dev, I have

  	        location /gb2 {
			proxy_pass http://localhost:9005;
		}	
		location /gbrowse2/i/ {
			alias /usr/local/wormbase/website/staging/extlib/gbrowse2/current/tmp/images/; 
		}
		
		location /gbrowse2/ {
			alias /usr/local/wormbase/website/staging/extlib/gbrowse2/current/html/; 
		}
 

GBrowse Configuration

header & footer

copy over the head header footer stanza in conf/gbrowse.conf/GBrowse.conf

Note: things might change in future as we change the header.

  # HTML to insert inside the <head></head> section
  head =  
    <script src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.4/jquery.min.js" type="text/javascript"></script> 
    <script src="http://ajax.googleapis.com/ajax/libs/jqueryui/1.8.6/jquery-ui.min.js" type="text/javascript"></script>   
    <script>
      var $jq=  jQuery.noConflict();
    </script>
    <script type="text/javascript" src="/js/raphael-min.js"></script>
    <script type="text/javascript" src="/js/layout.js" ></script>  
    <script type="text/javascript" src="/js/jquery/plugins/openid-selector-1.0/js/openid-jquery.js"></script>
    <link type="text/css" rel="stylesheet" href="/js/jquery/plugins/openid-selector-1.0/css/openid.css"/>
    <link media="screen" rel="stylesheet" href="/js/jquery/plugins/colorbox/example4/colorbox.css" />
    <script type="text/javascript" src="/js/jquery/plugins/colorbox/colorbox/jquery.colorbox-min.js"></script>
    <link type="text/css" href="/js/jquery/current-theme/development-bundle/themes/theme/jquery.ui.all.css" rel="stylesheet" />
    <link href="/css/main.css" rel="stylesheet" type="text/css" />  
    <link href="/css/home.css" rel="stylesheet" type="text/css" />
    <link type="text/css" href="/css/icons.css" rel="stylesheet" />

  # At the top of the HTML...
  header =  <div class="header"> </div>
	  <script type="text/javascript">
	      $jq(".header").load("/header",function() {
		  $jq.getScript('/js/ajax.js');
		  $jq.getScript('/js/nav.js');
		  $jq.getScript('/js/search.js');
	      });    
	  </script>
	 
  # At the footer
  footer = <div class='footer'></div>   
	 <script type='text/javascript'> 
	    $jq(".footer").load('/footer', function() {
		  $jq.getScript('/js/effect.js');
	      });    
	 </script> 

CSS

add stylesheet = /css/wormbase-gbrowse.css

This is needed for some css conflict between WormBase & GBrowse

URL change within APP itself

go into root/templates/config/external_urls 
   [% site.external_urls = {
	genomic_location = { description  = 'The WormBase Genome Browser'
			      maintainer   = ''
			      base         = '/gb2/gbrowse/'
			      search      = '/gb2/gbrowse/%s'   
			    }

	gbrowse_image = { description  = 'The WormBase Genome Browser Image'
			      maintainer   = ''
			      base         = '/gb2/gbrowse_img/'
			      search      = '/gb2/gbrowse_img/%s'   
			    }
  ...