Differences

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

--- sybil [2010/01/14 09:22] – 172.26.0.166
+++ 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 beig hosted at ILRI on request by [[http://igs.umaryland.edu/|IGS]].
-More information on Sybil can be found [[http://sybil.sourceforge.net/|here]].
-===== 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
-$ 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>
-===== Install Perl Dependencies =====
-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|EPEL]] (Extra Packages for Enterprise Linux) repository has been installed, as it has several modules we'll need.
-<file>
-            - 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</file>
-Log::Cabin
-===== 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>
-Wrong perl path!!! Change shebangs?!
-<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>