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--- post-assembly_analysis:banana_slug_genome_browser [2010/03/31 02:29]
galt
+++ post-assembly_analysis:banana_slug_genome_browser [2015/07/16 18:11]
ceisenhart
@@ Line 1: / Line 1: @@
-  * [[http://bananadev.cse.ucsc.edu/|Banana Slug Genome Browser]] will have a UCSC genome browser, once we get to the point of having few enough contigs that building a browser makes sense.
+======Banana slug genome browser======
-  * [[http://genome.ucsc.edu/admin/mirror.html|Mirroring the UCSC Genome Browser]] shows procedures for setting up a UCSC Genome Browser site. Although we are not trying to set up a mirror site, this still contains valuable configuration information.
+Currently the banana slug genome is supported as a private track hub. For those who know how to set up custom track hubs, the link is here. **If it is your first time setting up a custom track hub, follow the instructions for 'Mounting the banana slug track hub' below!**
-  * [[http://genomewiki.ucsc.edu/index.php/Minimal_Browser_Installation|Minimal Browser Install]] instructions are on the ucsc genomewiki.
-  * [[ http://genomewiki.ucsc.edu/index.php/Building_a_new_genome_database|Building a new genome database]] on the ucsc genomewiki.
+http://hgwdev-ceisenhart.cse.ucsc.edu/~ceisenhart/hubs/bananaSlug/hub.txt
-  * [[http://hgdownload.cse.ucsc.edu/admin/jksrc.zip|Source Code]] provides kent source zip.
-  * kent/src/product/README* has documentation on configuring and using the UCSC Genome Browser.
+Currently the following assemblies are supported;
-  * Internally, the Browser staff uses makeGenome.pl to automate much of the initial build of a browser for a new assembly.  The kent source contains that script and other scripts that it calls.
+ABySS
+SOAP
+Discovar //de novo//
+Mitochondrial
+===== Mounting the banana slug track hub =====
+To view the banana slug data please go to
+https://genome.ucsc.edu/cgi-bin/hgGateway
+and click the 'track hubs' button
+{{ ::firstbrowsershot.png |}}
+next navigate to the 'my hubs' tab
+{{ ::secondbrowsershot.png |}}
+Paste the url provided,
+http://hgwdev-ceisenhart.cse.ucsc.edu/~ceisenhart/hubs/bananaSlug/hub.txt
+into the 'URL' text box and click the 'Add hub' button.  You will be redirected to the banana slug hub which can be used as normal.
+=====Creating a new track hub=====
+To setup a custom track hub follow the instructions here.
+**Note the banana slug track hub has already been created.** These are the instructions that were used to create it the first time, it can be accessed using the instructions above.
+https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html

Banana Slug Genomics

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