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 cm_blast to sybil;
grant select on cm_cluster_members to sybil;
grant select on cm_clusters to sybil;
grant select on cm_proteins to sybil;
grant select on contact to sybil;
grant select on contact_relationship to sybil;
grant select on contactprop 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 cvtermprop to sybil;
grant select on cvtermsynonym to sybil;
grant select on db to sybil;
grant select on dbxref to sybil;
grant select on dbxrefprop to sybil;
grant select on environment to sybil;
grant select on environment_cvterm to sybil;
grant select on feature to sybil;
grant select on feature_cvterm to sybil;
grant select on feature_cvterm_dbxref to sybil;
grant select on feature_cvterm_pub to sybil;
grant select on feature_cvtermprop to sybil;
grant select on feature_dbxref to sybil;
grant select on feature_genotype to sybil;
grant select on feature_pub to sybil;
grant select on feature_relationship to sybil;
grant select on feature_relationship_pub to sybil;
grant select on feature_relationshipprop to sybil;
grant select on feature_relprop_pub 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 genotype to sybil;
grant select on incident to sybil;
grant select on incident_cvterm to sybil;
grant select on incident_dbxref to sybil;
grant select on incident_pub to sybil;
grant select on incident_relationship to sybil;
grant select on incidentprop to sybil;
grant select on infection to sybil;
grant select on infection_cvterm to sybil;
grant select on infection_dbxref to sybil;
grant select on infection_pub to sybil;
grant select on infectionprop to sybil;
grant select on organism to sybil;
grant select on organism_dbxref to sybil;
grant select on organismprop to sybil;
grant select on phendesc to sybil;
grant select on phenotype to sybil;
grant select on phenotype_comparison to sybil;
grant select on phenotype_comparison_cvt to sybil;
grant select on phenstatement to sybil;
grant select on phylonode to sybil;
grant select on phylonode_dbxref to sybil;
grant select on phylonode_organism to sybil;
grant select on phylonode_pub to sybil;
grant select on phylonode_relationship to sybil;
grant select on phylonodeprop to sybil;
grant select on phylotree to sybil;
grant select on phylotree_pub to sybil;
grant select on project to sybil;
grant select on pub to sybil;
grant select on pub_dbxref to sybil;
grant select on pub_relationship to sybil;
grant select on pubauthor to sybil;
grant select on pubprop to sybil;
grant select on stock to sybil;
grant select on stock_cvterm to sybil;
grant select on stock_dbxref to sybil;
grant select on stock_genotype to sybil;
grant select on stock_pub to sybil;
grant select on stock_relationship to sybil;
grant select on stock_relationship_pub to sybil;
grant select on stockcollection to sybil;
grant select on stockcollection_stock to sybil;
grant select on stockcollectionprop to sybil;
grant select on stockcollectionprop_stoc to sybil;
grant select on stockprop to sybil;
grant select on stockprop_pub to sybil;
grant select on synonym to sybil;
grant select on tableinfo to sybil;
grant select on transmission to sybil;
grant select on transmission_cvterm to sybil;
grant select on transmission_dbxref to sybil;
grant select on transmission_pub to sybil;
grant select on transmissionprop to sybil;

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

perl-MLDBM

Aspect

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