Learn about the Browser: Difference between revisions
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* The [http://genome-test.cse.ucsc.edu/eng/ old documentation website with developer documentation] | * The [http://genome-test.cse.ucsc.edu/eng/ old documentation website with developer documentation] | ||
* Compile Code/Install Data: | * Compile Code/Install Data: | ||
** [http://genome.ucsc.edu/admin/jk-install.html Compile the browser source code] | ** 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] | |||
** make sure you get those [[Build_Environment_Variables|environment variables right]] | ** make sure you get those [[Build_Environment_Variables|environment variables right]] | ||
** [http://genome.ucsc.edu/admin/mirror.html mirror a complete browser]. | ** [http://genome.ucsc.edu/admin/mirror.html mirror a complete browser]. | ||
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** See also the textfile README.building.source [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/README.building.source README.building.source] | ** See also the textfile README.building.source [http://hgwdev.cse.ucsc.edu/~kent/src/unzipped/product/README.building.source README.building.source] | ||
** [[Browser_Mirrors|Updating the data automatically from UCSC]] | ** [[Browser_Mirrors|Updating the data automatically from UCSC]] | ||
* | ** [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 | ||
* Load tracks into your browser: | * Load tracks into your browser: | ||
** [http://www.soe.ucsc.edu/~sugnet/doc/trackHowto/browserTalk.pdf Charles Sugnet's presentation about TrackDB] | ** [http://www.soe.ucsc.edu/~sugnet/doc/trackHowto/browserTalk.pdf Charles Sugnet's presentation about TrackDB] | ||
Revision as of 11:11, 2 December 2009
Documentation is still somewhat dispersed. Here are some starting points:
Use the browser website
- Video tutorials and slides by Openhelix
- Basic materials written by the gurus: The User's guide and the FAQs.
- A similar page to this one "Learning about the browser"
- Type in (manually) a couple of custom tracks in different formats
- Subscribe to the mailing list or search through it. Most everyday questions have already been asked by someone else so searching gives you an answer usually faster than asking on the mailing list.
Access the data of the genome browser and process them on your machine
- Be aware that internal coordinates (not website) are 0-based!
- 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):
- Public mysql access
- The all.joiner file, describes relations between all database tables
- For all genes-related tables, there is a graphical map (sub-optimal layout :-)
- Flat-file data (in /gbdb and on the ftp server)
Installling the browser locally on your own Unix machine and extend it
- The old documentation website with developer documentation
- Compile Code/Install Data:
- What is the the source tree ?
- What is available in the Kent source utilities ?
- Compile the browser source code
- make sure you get those environment variables right
- mirror a complete browser.
- When you run into problems, search through the mailing list when you have problems and read the documentation in the directory kent/src/product
- some hints for MacOS users
- See also the textfile README.building.source README.building.source
- Updating the data automatically from UCSC
- searching through the archives or the Technical-FAQ-Category of the wiki when you have problems
- Load tracks into your browser:
- How UCSC folks created their tracks:
- UCSC's makeDb-files
- Some explanations how to read their files: bashVsCsh
- a similar place with hgSearchSpec docs and statistics (the system to search for ids) can be found completely off-track
- Sequence your genome of interest and create a browser for it
- Whole-genome alignment pipeline: Angies mental model and Max's howto
