Differences

This shows you the differences between two versions of the page.

--- sybil [2010/07/22 19:20] – 172.26.15.75
+++ sybil [2010/09/04 00:54] (current) – removed aorth
@@ Line 1: / Line 1: @@
-===== Sybil =====
-Sybil is a web-based software package for comparative genomics. The version installed at ILRI is specific for Streptococcus pneumoniae. It is being hosted at ILRI on request by the [[http://igs.umaryland.edu/|IGS]].
-More information on Sybil can be found [[http://sybil.sourceforge.net/|here]].
-http://sybil.ilri.cgiar.org/  is a Virtual Machine with IP address is 172.26.100.101
-===== Installation =====
-  * [[#Install PostgreSQL|Install PostgreSQL]]
-  * [[#Install Perl Dependencies|Install Perl Dependencies]]
-===== Install PostgreSQL =====
-Install and start the PostgreSQL server:
-<code>$ sudo yum install postgresql-server postgresql-devel
-$ sudo service postgresql start</code>
-Switch to the ''postgre'' user:
-<code>$ sudo su - postgres</code>
-Create an empty database for Strepneumo:
-<code>$ createdb strepneumo</code>
-Import the Strepneumo database dump:
-<code>$ zcat strepneumo_v10.dump.gz | psql -d strepneumo -f -</code>
-Optimize the database:
-<code>$ vacuumdb -d strepneumo --full --analyze --echo</code>
-Create a user for sybil:
-<code>$ psql
-postgres=# create user sybil;
-postgres=# ALTER USER sybil WITH ENCRYPTED PASSWORD '!lr!9Rockz';</code>
-Set permissions on the strepneumo db for the Sybil user:
-<file>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;</file>
-<file>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;</file>
-===== Install Perl Dependencies =====
-The ''INSTALL'' file lists Perl dependencies that need to be installed.  Use CPAN to install them:
-<file>
-            - Bio::Perl
-            - 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
-            - MLDBM
-            - JSON
-            - Aspect
-            - Benchmark::Timer</file>
-===== Install Sybil HTML =====
-Install the web server components of Sybil:
-<code># cp -R htdocs/ /var/www/html/sybil
-# cp -R cgi-bin/ /var/www/cgi-bin/sybil</code>
-Create the cache directory for sybil and make sure the web server can write there:
-<code># mkdir /var/www/html/sybil/img_cache
-# chown apache /var/www/html/sybil/img_cache
-# chmod 755 /var/www/html/sybil/img_cache</code>
-The perl path is wrong in the installed scripts, change it:
-<code># find /var/www/cgi-bin/ -iname "*.pl" -exec sed -i 's/\/local//' {} \;</code>
-==== Firewall Rule for Apache ====
-<file>-A RH-Firewall-1-INPUT -m state --state NEW -m tcp -p tcp --dport 80 -j ACCEPT</file>
-===== Graphviz =====