Learn about the Browser: Difference between revisions

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** [[Cookie_Session|How are cookies handled by the browser?]]
** [[Cookie_Session|How are cookies handled by the browser?]]
** It seems that you can also run a mirror on windows (see [https://lists.soe.ucsc.edu/pipermail/genome-mirror/2008-November/001059.html]) but your mileage may vary to get everything to compile. If you have one running, please update this wiki.
** It seems that you can also run a mirror on windows (see [https://lists.soe.ucsc.edu/pipermail/genome-mirror/2008-November/001059.html]) but your mileage may vary to get everything to compile. If you have one running, please update this wiki.
== UCSC source tools to analyze genomics data on your own machine ==
** What is the [[the source tree]] ?
** What is available in the [[Kent source utilities]] ?
** Download the most important [http://hgdownload.cse.ucsc.edu/admin/exe/ compiled binary programs]
** [http://genome.ucsc.edu/admin/jk-install.html Compile all tools (includes the browser webserver)] yourself
** You need to set some [[Build_Environment_Variables|environment variables]] before you start the compilation
** Walkthroughs for...
*** [http://bergman-lab.blogspot.com/2009/03/compiling-ucsc-source-tree-utilities-on.html MacOS X users]
*** [[Source tree compilation on Debian/Ubuntu|Debian and Ubuntu]]
** The most common problem on the mailing list are harmless warnings that trigger errors. To ignore these, which is usually safe, [https://lists.soe.ucsc.edu/pipermail/genome-mirror/2006-November/000251.html remove the -Wall option from the makefile]
** See also the textfile README.building.source [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/README.building.source README.building.source]
** [http://genome.ucsc.edu/contacts.html searching through the archives] or the [[:Category:Technical FAQ| Technical-FAQ-Category of the wiki]] when you have problems


== Modify your own copy of the browser ==
== Modify your own copy of the browser ==
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* Create a browser for a [[Building a new genome database|completely new genome]]
* Create a browser for a [[Building a new genome database|completely new genome]]


== Compile the source tree to get your own genomics pipeline started ==
** What is the [[the source tree]] ?
** What is available in the [[Kent source utilities]] ?
** [http://genome.ucsc.edu/admin/jk-install.html Compile the browser source code]
** You need to set some [[Build_Environment_Variables|environment variables]] before you start the compilation
** Walkthroughs for...
*** [http://bergman-lab.blogspot.com/2009/03/compiling-ucsc-source-tree-utilities-on.html MacOS X users]
*** [[Source tree compilation on Debian/Ubuntu|Debian and Ubuntu]]
** The most common problem on the mailing list are harmless warnings that trigger errors. To ignore these, which is usually safe, [https://lists.soe.ucsc.edu/pipermail/genome-mirror/2006-November/000251.html remove the -Wall option from the makefile]
** See also the textfile README.building.source [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/README.building.source README.building.source]
** [http://genome.ucsc.edu/contacts.html searching through the archives] or the [[:Category:Technical FAQ| Technical-FAQ-Category of the wiki]] when you have problems


== Making Of: How the UCSC genome annotations are created ==
== Making Of: How the UCSC genome annotations are created ==

Revision as of 10:30, 18 January 2010

This list is sorted by increasing technical complexity: the first steps require only a webbrowser, the last ones a Linux webserver.

Use the browser website

Access the data of the genome browser and process them on your machine

  • Be aware that internal coordinates (not website) are 0-based!
  • Unlike Gbrowse and Ensembl, UCSC is storing the data partially in SQL (coordiantes, outline of x-y-plots) and partially in flat text files (sequences, alignments, details of x-y-plots)
  • Table Browser: The easiest way to access data (you don't have to care whether data is stored in MySQL or in textfiles):
  • SQL-stored data (FAQ):
  • Flat-file data: Download from the ftp server (stored in /gbdb on browser servers)

Install a copy of the browser on your own machine (Unix or Mac, Windows optional)

UCSC source tools to analyze genomics data on your own machine

Modify your own copy of the browser


Making Of: How the UCSC genome annotations are created

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