From: anja <fri...@ho...> - 2010-10-05 21:24:51
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Hi Mitch, when I visit http://localhost/ then I see the surface of JBrowse and the track as a grey line, so no motifs at all... more then before I guess Anja Date: Tue, 5 Oct 2010 14:15:32 -0700 From: ml-...@n3... To: fri...@ho... Subject: Re: data are not displayed even though they were loaded (JBrowse) E-Mail-Text I'm not totally sure what's going on for you, but here's my best guess: Usually, web servers are set up so that one particular path (e.g., /var/www) becomes the "root" of the space on the web server. So, for example, if you put a file named "foo.html" into /var/www, so that the full path is /var/www/foo.html, then it'll show up in the web server as /foo.html. So if you're accessing the web server on your laptop, you can see that HTML page by going to http://localhost/foo.html. Different linux distributions put the "root" of the web server space in different places; in ubuntu (and distributions based on ubuntu, like Mint), it's /var/www. In distributions derived from Red Hat, it's /var/www/html. In your case, it looks like it's /var/www, so if you want to see what's in /var/www, you can visit http://localhost/ in your web browser. If you look there, do you see your data? Mitch On 10/04/2010 11:52 AM, Anja Friedrich wrote: Hi all, I was using SeqFeature Store to load data and display them in JBrowse. But I an't see anything. They are not displayed at all like they don't exist... Do I activate it wrong? I was looking under http://localhost/jbrowse/ I used this commandos and it looks as if the data were loaded... anou@anou-laptop:/var/www$ bp_seqfeature_load.pl --d "dbi:Pg:dbname=test" --a DBI::Pg --c taro.gff loading taro.gff... 98 features loaded in 0.41s Building object tree... 0.02s load time: 0.46s anou@anou-laptop:/var/www$ bin/prepare-refseqs.pl --conf taro.json --refs NC_010109.1 anou@anou-laptop:/var/www$ bin/biodb-to-json.pl --conf taro.json working on refseq NC_010109.1 working on track nested_tandem_repeat got 1 features for nested_tandem_repeat anou@anou-laptop:/var/www$ bin/generate-names.pl Anja ------------------------------------------------------------------------------ Virtualization is moving to the mainstream and overtaking non-virtualized environment for deploying applications. Does it make network security easier or more difficult to achieve? Read this whitepaper to separate the two and get a better understanding. http://p.sf.net/sfu/hp-phase2-d2d _______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax ------------------------------------------------------------------------------ Beautiful is writing same markup. Internet Explorer 9 supports standards for HTML5, CSS3, SVG 1.1, ECMAScript5, and DOM L2 & L3. Spend less time writing and rewriting code and more time creating great experiences on the web. Be a part of the beta today. http://p.sf.net/sfu/beautyoftheweb _______________________________________________ Gmod-ajax mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-ajax View message @ http://gmod.827538.n3.nabble.com/Gmod-ajax-data-are-not-displayed-even-though-they-were-loaded-JBrowse-tp1631655p1638798.html To start a new topic under GMOD, email ml-...@n3... To unsubscribe from GMOD, click here. -- View this message in context: http://gmod.827538.n3.nabble.com/Gmod-ajax-data-are-not-displayed-even-though-they-were-loaded-JBrowse-tp1631655p1638868.html Sent from the JBrowse mailing list archive at Nabble.com. |