Banana Slug Genomics

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====== Installing the UCSC Genome Browser ======

Patricia Chan gave a lecture on setting up the UCSC Genome Browser.
{{:lecture_notes:genomebrowsersetup.pdf|}}
===== UCSC Genome Browser =====
==== Requirements ====
  * 32/64 bit Linux/Unix system
  * CGI
  * MySQL database
  * Apache

Written in C and JavaScript (JQuery)

To install or mirror a genome browser on a new server:
http://genomewiki.ucsc.edu/index.php/Browser_Installation


==== Where are the data? ====
  * MySQL Database
    * Each genome assembly has its own database
    * Most track data stored in MySQL

  * ''/gbdb/<DB name>''
    * Each genome assembly has its own local directory
    * sequences, wiggle track data, other large data sources (.bam files)

''centraldb''
  * Contains all genome information.
  * ''centraldb.dbDb'' stores the information
  * ''centraldb.blatservers'' stores the info for two blat servers (one of DNA, one for protein sequences)
  * Can be renamed in ''.hg.conf''

Track Info
  * Stored in the ''trackDb'' table in each genome's MySQL database.
  * Based on ''trackDb.ra'' files as input source.
  * The global ''trackDb.ra'' contains tracks that apply to multiple genomes.
  * Similar to building a custom track on the genome browser.

Kent Code Base
  * Required to set up the browser.
  * Latest source code is in GIT repository.
  * Need a CGI sandbox. 
  * ''make utils'' in ''~/kent/src''
  * Binaries are installed in ''~/bin/${MACHTYPE}''

Browser Configuration File
  * ''.hg.conf''
  * Contains MySQL user accounts and passwords, ''centraldb'' info, ''trackDb'' info.
  * Required by Kent applications to connect to MySQL.

===== Install the Genome Browser =====
==== Prepare Genome Sequences ====
  * Create ''/gbdb/newGenome'' directory for a new genome assembly
  * Convert genome sequences from FASTA to 2bit format.
    * ''faToTwoBit chr1.fa [chr2.fa ...] /gbdb/newGenome/newGenome.2bit''
  * FASTA input files must have UNIX LF character.

==== Setup Genome Database ====
  * create a MySQL database for the genome assembly:
    * ''hgsql "" -e "create database if not exists newGenome"''
    * ''hgsql'' is a wrapper for passing SQL commands. The first argument is the database name.
  * create a group table for the new database
    * ''cd ~/kent/src/hg/lib''
    * ''hgsql newGenome < grp.sql''
  * create a chromInfo table
    * ''faSize -detailed chr1.fa [chr2.fa ...] > chrominfo.tab''
    * ''hgsql newGenome < ~/kent/src/hg/lib/ chromInfo.sql''
    * ''hgsql newGenome -e 'load data local infile "chrominfo.tab" into table chromInfo;"''
    * ''hgsql newGenome -e 'update chromInfo set fileName = "/gbdb/newGenome/newGenome.2bit"''

==== Make New Genome Available ====
  * Add an entry into the ''centraldb.dbDb'' table
  * Add an entry into the ''centraldb.defaultDb'' table
    * Set the default assembly to use.
  * Add an entry into the ''centraldb.genomeClade'' table
    * The clade the genome is associated with.
    * If the genome belongs to a clade that is not in the browser, add an entry to the ''centraldb.clade'' table.
  * Add a description of the genome in an HTML file (''/gbdb/newGenome/html/description.html'')
    * Free formatted.

===== Configuration =====

==== Track Configuration ====
  * Each genome database needs a trackDb table
  * the global trackDb.ra is in ''~/kent/src/hg/makeDb/trackDb''
  * genome specific trackDb.ra is stored in ''~/kent/src/hg/makeDb/trackDb/<DB name>''
    * can be stored in an alternate location.

==== Search Configuration ====
  * a ''hgFindSpec'' table is required for specifying search criteria.
  * Search criteria for each track are also loaded from ''trackDb.ra''.

==== Start BLAT Server ====
  * To run BLAT, gfServer for each genome must be started.
  * Insert 2 records into ''centraldb.blatServers'' table.
  * Make sure port numbers are different.
  * If BLAT server is not run locally
    * ''rsync -v /gbdb/newGenome/newGenome.2bit blat_host:/gbdb/newGenome''
  * At the host machine, start BLAT server in the background.

===== Automation =====
  * The previous steps are automated in the perl script ''make-browser''.
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