Installing Chado on Ubuntu HOWTO

Ubuntu version

This method has been tested on Ubuntu 8.4 with PostgreSQL 8.1 and on Ubuntu 11.10 and 12.04 with PostgreSQL 9.1. Note also that starting with the 12.10 Ubuntu release (October, 2012) this became even easier since a Debian package for Chado (libchado-perl) was added to the official repository making installation a real snap. That package is available for Debian installations as well.


Installing prereqs with Synaptic:

sudo apt-get install postgresql postgresql-client postgresql-contrib postgresql-plperl libpq-dev libdbd-pg-perl libtemplate-perl libxml-simple-perl liblog-log4perl-perl ant libparse-recdescent-perl xsltproc bioperl

Create a db user for yourself - your Ubuntu username:

 $ sudo su - postgres
 $ createuser <username>
 Shall the new role be a superuser? (y/n) y
 $ vi /etc/postgresql/9.1/main/pg_hba.conf
 #changed "local all all" and "host all all" lines from ident sameuser to trust
 $ exit
 $ sudo /etc/init.d/postgresql restart

It is useful to actually have a password, even using trust, otherwise problems with DBD::Pg pop up telling you that no password was supplied.

 $ sudo su - postgres
 $ psql -d template1
 $ alter USER <username> with password '<password>';
 $ exit #from psql
 $ exit #from sudo

Installing prereqs with cpan shell:

Installed DBIx::DBStag ‘by hand’:

(Note that if you have the cpan shell set up to do “sudo make” rather than running the whole shell as root (via “sudo cpan”), you can install DBIx::DBStag from the cpan shell.)

 tar zxvf DBIx-DBStag-0.10.tar.gz
 cd DBIx-DBStag-0.10
 createdb test   # needed for the make test step
 perl Makefile.PL
 make test  #all tests pass
 sudo make install

Create the file ~/.gmod_profile, with the contents:

 export GMOD_ROOT=/usr/local/gmod
 export CHADO_DB_NAME=chado
 export CHADO_DB_USER=<username>
 export CHADO_DB_PASS=<password>
 export CHADO_DB_HOST=localhost
 export CHADO_DB_PORT=5432
 export GO_ROOT=/usr/local/share/perl/5.8.8/GO

and add this line to the end of ~/.bash_profile:

 . ~/.gmod_profile   #sources the gmod profile on login

If you haven’t already, download gmod, either from

or via SVN.

Then, in the gmod directory

 perl Makefile.PL
 sudo make install
 make load_schema
 make prepdb
 make ontologies  #selected 1,2,3,4

Get and load yeast GFF3 file:

  wget --analysis --organism=yeast -g saccharomyces_cerevisiae.gff --noexon