ILRI Research Computing

Sybil is a web-based software package for comparative genomics. The version installed at ILRI is specific for Streptococcus pneumoniae. It is beig hosted at ILRI on request by IGS.

More information on Sybil can be found here.

• Install PostgreSQL
• Install Perl Dependencies

Install and start the PostgreSQL server:

$ sudo yum install postgresql-server
$ sudo service postgresql start

Switch to the postgre user:

$ sudo su - postgres

Create an empty database for Strepneumo:

$ createdb strepneumo

Import the Strepneumo database dump:

$ zcat strepneumo_v10.dump.gz | psql -d strepneumo -f -

Optimize the database:

$ vacuumdb -d strepneumo --full --analyze --echo

The INSTALL file lists Perl dependencies that need to be installed. Some can be installed via package manager, but others will need to be manually installed via CPAN. First, make sure the EPEL (Extra Packages for Enterprise Linux) repository has been installed, as it has several modules we'll need.

            - bioperl 1.4
            - DBI
            - DBD::Pg
            - GD
            - GD::SVG
            - SVG
            - Graph::Kruskal
            - LWP::UserAgent
            - HTTP::Request
            - XML::Simple
            - XML::Parser
            - XML::Simple
            - XML::Writer
            - Tree::DAG_Node
            - File::Spec
            - Storable
            - Date::Manip
            - Date::Format
            - Log::Log4perl
            - MIME::Lite
            - Time::HiRes

Install the web server components of Sybil:

# cp -R htdocs/ /var/www/html/sybil
# cp -R cgi-bin/ /var/www/cgi-bin/sybil

Create the cache directory for sybil and make sure the web server can write there:

# mkdir /var/www/html/sybil/img_cache
# chown apache /var/www/html/sybil/img_cache
# chmod 755 /var/www/html/sybil/img_cache

Wrong perl path!!! Change shebangs?!

-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 80 -j ACCEPT