Difference between revisions of "Design Specs: GBrowse Integration"
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− | + | = 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> | ||
− | + | = 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> | ||
− | + | ||
+ | = 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
Contents
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
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' } ...