Install coge

Server with existing CoGe Installation

Create new mysql database

Dump CoGe Database schema

• File download: http://data.iplantcollaborative.org/quickshare/71b18508287f9fb0/cogetable.sql (AUTO_INCREMENT removed)

mysqldump -d -h localhost -u root -pXXXXXXX coge | sed 's/AUTO_INCREMENT=[0-9]*\b/AUTO_INCREMENT/' > cogetable.sql

Create new CoGe Database

create database oryza_coge

Initialize new coge database

mysql -u root -pXXXXXXXX oryza_coge < cogetable.sql

Populate a few entries in the feature_type table

• This is important because part of CoGe's code-base is keyed to feature_type_ids. This is done in order to improve performance of the system by using a feature_type_id to retrieve features of a particular type. An example is OrganismView which needs to find features of type "chromosome" in order to determine the size of a genome. The table loaded here contains 10 feature types
• Download file: http://data.iplantcollaborative.org/quickshare/ac8758f83c9b29b1/feature_type.sql

mysql -u root -pXXXXXXXXX oryza_coge < feature_type.sql

Create new user for new CoGe database

• Want a web-user with limited write privileges and a power user to load new data

create user 'oryza_coge'@'localhost' IDENTIFIED BY 'XXXXXX';
grant all privileges on oryza_coge.* to oryza_coge;
create user 'oryza_coge_web'@'localhost' IDENTIFIED BY 'XXXXXX';
grant select on oryza_coge.* to oryza_coge_web;
flush privileges;

Note: The CoGe web-user needs edit/insert permission on some tables. Here is a snapshot of what these are:

Deploy new CoGe Web-site

Download CoGe repository from GitHub

git clone https://github.com/LyonsLab/coge.git

Make directories where files go and give write persmission

cd web
./setup.sh

Configure apache

sudo vi /etc/apache2/sites-enabled/000-default

##Configure the main website
Alias /Oryza_CoGe "/opt/apache2/Oryza_CoGe"
Alias /oryza_coge "/opt/apache2/Oryza_CoGe"
Alias /oCoGe "/opt/apache2/Oryza_CoGe"
Alias /ocoge "/opt/apache2/Oryza_CoGe"
<Directory "/opt/apache2/Oryza_CoGe">
  PerlInitHandler Apache2::Reload
  Options Includes Indexes ExecCGI FollowSymLinks
  AllowOverride AuthConfig
  SetEnv HOME "/opt/apache2/Oryza_CoGe/"
  Order allow,deny
  Allow from all
</Directory>

<Directory /home/mbomhoff/public/coge/services/JBrowse/JBrowse_TrackContent_WS/>
   Options FollowSymLinks +ExecCGI
   AddHandler wsgi-script .py
</Directory>
Alias /coge/services/JBrowse/track /home/mbomhoff/public/coge/services/JBrowse/JBrowse_TrackContent_WS/source.py

<Directory /opt/apache2/Oryza_CoGe/services/JBrowse/JBrowse_TrackContent_WS/>
   Options FollowSymLinks +ExecCGI
   AddHandler wsgi-script .py
</Directory>
Alias /Oryza_CoGe/services/JBrowse/track /Oryza_CoGe/services/JBrowse/JBrowse_TrackContent_WS/source.py

##configure gobe (visualization tool for GEvo)
<Directory "/opt/apache2/Oryza_CoGe/gobe/">
   Options FollowSymLinks +ExecCGI
   AddHandler wsgi-script .py
</Directory>

Configure coge.conf file

##This is a configuration file for CoGe.  
##Key Value pairs:
##<NAME>    <PATH>

#database configuration
DBNAME    oryza_coge
DBHOST    localhost
DBPORT    3306
DBUSER    oryza_coge_web
DBPASS    XXXXXXXXXXXX

#basedir for coge
COGEDIR     /opt/apache/Oryza_CoGe/

#bin dir for coge's programs
BINDIR      /opt/apache/Oryza_CoGe/bin/ 

#data dir for coge's programs
DATADIR     /opt/apache/Oryza_CoGe/data/ 

#dir for pair-wise whole genome comparisons (e.g. SynMap)
DIAGSDIR            /opt/apache/Oryza_CoGe/diags/ 

#fasta dir
FASTADIR            /opt/apache/Oryza_CoGe/data/fasta/

#TMPL dir for coge's web page templates
TMPLDIR     /opt/apache/Oryza_CoGe/tmpl/

#temp dir for coge
TEMPDIR   /opt/apache/Oryza_CoGe/tmp/

#Base URL for web-site
URL         /Oryza_CoGe/

#URL for temp directory
TEMPURL     /Oryza_CoGe/tmp/

#blast style scoring matrix dirs
BLASTMATRIX    /opt/apache/Oryza_CoGe/data/blast/matrix/

#blastable DB
BLASTDB    /opt/apache/Oryza_CoGe/data/blast/db/

#directory for bed files
BEDDIR     /opt/apache/Oryza_CoGe/data/bed/

#servername for links
SERVER      http://coge.iplantcollaborative.org/Oryza_CoGe/

#directory for caching genome browser images
IMAGE_CACHE /opt/apache/Oryza_CoGe/data/image_cache/

Install Perl Modules

• The subdirectories in modules/ from which you should install are:
  • Accessory
  • Algos
    • Codeml
    • KsCalc
    • Pairwise
  • Graphics
  • Database

perl Makefile.PL lib=/usr/local/lib/perl; make install

Install JBrowse

Download and install the JBrowse package from http://jbrowse.org/install/

cd js
unzip JBrowse-1.9.7.zip
mv JBrowse-1.9.7 jbrowse

Populate with test data

scripts/replicate_genome_between_coge_installations.pl -dsgid 11022 -u1 coge -p1 XXXXXXX -db1 coge -u2 oryza_coge -p2 XXXXXXX -db2 oryza_coge -sd /opt/apache/oryz_coge/data/genomic_sequence

Troubleshooting

Visualization in GEvo does not work

This relies on a system known as Gobe. Check the following things:

• Apache configuration for gobe
• Check to see if paths hard-coded into gobe/flash/service.wsgi need to be updated
  • NOTE: Not sure if this is required