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- Configure Apache:
service mysqld start
chkconfig httpd on
chkconfig mysqld oni
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- Getting web files:
cd /usr/lib64
ln -s libcrypto.so.10 libcrypto.so.6
ln -s libssl.so.10 libssl.so.6
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- hgFixed DB:
mysql> create database hgcentral
mysql --[mysqlaccessoptions] hgcentral < hgcentral.sql
mysql --[mysqlaccessoptions] -e "create database hgFixed"- hg19 DB:
mysql> CREATE DATABASE hg19
- BD Permisions:cd /var/lib/mysql/hg19rsync -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* .
GRANT SELECT, CREATE TEMPORARY TABLESON hgcentral.*TO readonly@localhostIDENTIFIED BY'access';
GRANT SELECT, INSERT, UPDATE, DELETE, CREATE, DROP, ALTERON hgcentral.*TO readwrite@localhostIDENTIFIED BY'update';
GRANT SELECT, CREATE TEMPORARY TABLESON hg19.*TO readonly@localhostIDENTIFIED BY'access';
GRANT SELECT, CREATE TEMPORARY TABLESON hgFixed.*TO readonly@localhostIDENTIFIED 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
