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
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'
}
...
