Install UCSC Genome Browser

Introduction:

How to install a minimal installation of UCSC Genome Browser on Centos6 x86_64 with in a custom directory.

Steps:

- Install apache and mysql:

 yum install httpd mysql-server mysql

- Start services:

service httpd start
service mysqld start
chkconfig httpd on
chkconfig mysqld oni

- Configure Apache:

cd /var/www
mkdir html

mkdir cgi-bin

Create a config file like: /etc/httpd/conf.d/ucsc_genomebrowser.conf:

#
# UCSC GENOME BROWSER
#

<Directory "/var/www/ucsc-genomebrowser/html">
     Order Allow,Deny
     Allow from all
</Directory>

<Directory "/var/www/ucsc-genomebrowser/cgi-bin">
     AllowOverride None
     Options None
     Order allow,deny
     Allow from all
</Directory>

XBitHack on
<Directory "/var/www/ucsc-genomebrowser/html">
     Options +Includes
</Directory>

ScriptAlias /genomebrowser/cgi-bin /var/www/ucsc-genomebrowser/cgi-bin
Alias /genomebrowser /var/www/ucsc-genomebrowser/html
Alias /style /var/www/ucsc-genomebrowser/html/style

Reload Apache: service httpd restart

- Preparing the system:

Execute and add to /etc/profile:

    export WEBROOT=/var/www/ucsc-genomebrowser/html
    export CGI_BIN=/var/www/ucsc-genomebrowser/cgi-bin
    export MYSQLDATA=/var/lib/mysql

cd /usr/local/
mkdir apache
cd apache/
ln -s /var/www/ucsc-genomebrowser/html/ htdocs

yum install openssl
cd /usr/lib64
ln -s libcrypto.so.10 libcrypto.so.6
ln -s libssl.so.10 libssl.so.6

- Getting web files:

rsync -avzP rsync://hgdownload.cse.ucsc.edu/cgi-bin/ $CGI_BIN
rsync -avzP rsync://hgdownload.cse.ucsc.edu/htdocs/ $WEBROOT/

mkdir  /gbdb
cd /gbdb
mkdir -p hg19/nib
cd hg19/nib

rsync -avzP --delete --max-delete=20 rsync://hgdownload.cse.ucsc.edu/gbdb/hg19/hg19.2bit .
cd  /gbdb/hg19/
ln -s nib/hg19.2bit
chcon -R unconfined_u:object_r:httpd_sys_script_exec_t:s0 /gbdb
chown -R apache.apache /gbdb/

- Set up the Database:
  - hgcentral DB:

wget http://hgdownload.cse.ucsc.edu/admin/hgcentral.sql
mysql> create database hgcentral
mysql --[mysqlaccessoptions] hgcentral < hgcentral.sql

   - hgFixed DB:

mysql --[mysqlaccessoptions] -e "create database hgFixed"

  - hg19 DB:

mysql> CREATE DATABASE hg19

cd /var/lib/mysql/hg19

rsync -avP rsync://hgdownload.cse.ucsc.edu/mysql/hg19/grp* .
rsync -avP rsync://hgdownload.cse.ucsc.edu/mysql/hg19/trackDb* .
rsync -avP rsync://hgdownload.cse.ucsc.edu/mysql/hg19/hgFindSpec* .
rsync -avP rsync://hgdownload.cse.ucsc.edu/mysql/hg19/chromInfo* .

rsync -avP rsync://hgdownload.cse.ucsc.edu/mysql/hg19/gold* .

rsync -avP rsync://hgdownload.cse.ucsc.edu/mysql/hg19/gap* .

- BD Permisions:

GRANT SELECT, CREATE TEMPORARY TABLES

  ON hgcentral.*

  TO readonly@localhost

  IDENTIFIED BY 'access';

GRANT SELECT, INSERT, UPDATE, DELETE, CREATE, DROP, ALTER

  ON hgcentral.*

  TO readwrite@localhost

  IDENTIFIED BY 'update';

 

GRANT SELECT, CREATE TEMPORARY TABLES

  ON hg19.*

  TO readonly@localhost

  IDENTIFIED BY 'access';

GRANT SELECT, CREATE TEMPORARY TABLES

  ON hgFixed.*

  TO readonly@localhost

  IDENTIFIED BY 'access';

 - Getting config file:

wget http://genome-test.cse.ucsc.edu/~kent/src/unzipped/product/ex.hg.conf
mv ex.hg.conf /var/www/ucsc-genomebrowser/cgi-bin/hg.conf

chmod 600 /var/www/ucsc-genomebrowser/cgi-bin/hg.conf
chown apache.apache /var/www/ucsc-genomebrowser/cgi-bin/hg.conf
chcon unconfined_u:object_r:httpd_sys_script_exec_t:s0 /var/www/ucsc-genomebrowser/cgi-bin/hg.conf

- Configuring:

Change users and passwords (readonly/access and readwrite/update)
[...]
defaultGenome=hg19
[...]

-Trash:

mkdir /var/www/ucsc-genomebrowser/trash
chown apache:apache /var/www/ucsc-genomebrowser/trash

REFERENCES:

http://genome.ucsc.edu/admin/mirror.html
http://bergmanlab.smith.man.ac.uk/?p=1111
http://genomewiki.ucsc.edu/index.php/Browser_Installation
http://genomewiki.ucsc.edu/index.php/Minimal_Browser_Installation