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

Create a user for sybil:

$ psql
postgres=# create user sybil;
postgres=# ALTER USER sybil WITH ENCRYPTED PASSWORD '!lr!9Rockz';

Set permissions on the strepneumo db for the Sybil user:

grant select on analysis to sybil;
grant select on analysisfeature to sybil;
grant select on analysisprop to sybil;
grant select on author to sybil;
grant select on contact to sybil;
grant select on cv to sybil;
grant select on cvterm to sybil;
grant select on cvterm_dbxref to sybil;
grant select on cvterm_relationship to sybil;
grant select on cvtermpath to sybil;
grant select on cvtermsynonym to sybil;
grant select on db to sybil;
grant select on dbxref to sybil;
grant select on feature to sybil;
grant select on feature_cvterm to sybil;
grant select on feature_dbxref to sybil;
grant select on feature_pub to sybil;
grant select on feature_relationship to sybil;
grant select on feature_synonym to sybil;
grant select on featureloc to sybil;
grant select on featureprop to sybil;
grant select on featureprop_pub to sybil;
grant select on organism to sybil;
grant select on organism_dbxref to sybil;
grant select on organismprop to sybil;
grant select on project to sybil;
grant select on pub to sybil;
grant select on pub_author to sybil;
grant select on pub_dbxref to sybil;
grant select on pub_relationship to sybil;
grant select on pubprop to sybil;
grant select on synonym to sybil;
grant select on tableinfo to sybil;

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

Log::Cabin

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

The perl path is wrong in the installed scripts, change it:

# find /var/www/cgi-bin/ -iname "*.pl" -exec sed -i 's/\/local//' {} \;

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