HuRef Genome Browser Files

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  WARNING
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  There is no funding or support for this software, and
  there is minimal documentation.
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HuRef Genome Browser
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This document describes how to get started using the HuRef 
genome browser currently at http://huref.jcvi.org

1. Download HuRef databases
2. Installation
3. How the code is organized
4. Contact


1. Download HuRef databases
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The HuRef browser is designed to be run off of a Chado database 
(see http://gmod.org/wiki/Chado).  The HuRef database generally
follows the GMOD conventions with some modifications.

Download the HuRef databases at 
ftp://ftp.jcvi.org/pub/data/huref/databases/


2. Installation
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This installation process has not been tested, but it should work.

a. Install PostgreSQL version 8.x

b. Create sample databases
   psql -c "CREATE DATABASE huref6"
   psql -c "CREATE DATABASE homo_sapiens_core_41_36c"
   
c. Create database user accounts
   See http://www.postgresql.org/docs/8.0/interactive/sql-createuser.html
   
c. Restore the HuRef databases
   bzcat homo_sapiens_core_41_36c.20090806.sql.bz2 | psql homo_sapiens_core_41_36c
   bzcat huref6.20090806.sql.bz2 | psql huref6
   See http://www.postgresql.org/docs/8.0/interactive/backup.html
	
d. Grant SELECT privileges to your database user account
   The browser requires a database user account with SELECT 
   privileges to all of the tables in the databases.
   See http://www.postgresql.org/docs/8.0/interactive/sql-grant.html
   
e. Configuration
   Update the huref-conf/defaults.conf to point to your installation of these 
   databases, with your database login info.
   
f. Test the data and image generation
   cd huref-web
   ./fetchData.pl search=chr19:57550000+40000
   
   The above command should produce some JSON-formatted output that the Javascript
   code calls and uses to render the display.  In addition, it writes the required
   images to the huref-web/images/viewer/ directory.  If the JSON output is generated
   and you see .jpg files and .map files in the viewer directory, the browser
   should work fine.
   
g. Point your Apache hdocument root to huref-web
   That's it.  You should now have a replication of http://huref.jcvi.org
   
h. Use your own custom data
   There was no funding to built a "generic" genome browser.  However, as long 
   as you follow the data loading and storage conventions, you should be able 
   to use the browser on your genome data.  This has not been done or tested yet.
   Let us know if you successfully do so.


3. How the code is organized
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- huref-api
The API for all of the HuRef classes

- huref-bioperl
Same as BioPerl except a handful of HuRef glyphs that we added
in Bio::Graphics::Glyph::Huref*

- huref-conf
Contains the configuration file, plus an indexed db file used
for the Haplotype track.

- huref-web
The web tier, the user should have a symbolic link or simply
point the Apache document root to this directory.

- huref-chado
Contains the directory of database loaders for assembly (Celera assembler output),
karyotype bands, Ensembl data, HUGO, OBO ontologies, OMIM, RefSeq.


3. Contact us
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You can feel free to contact us

Nelson Axelrod naxelrod@jcvi.org

Yuan Lin ylin@jcvi.org

We make no promises of support, but we'll try to help as time permits.