Debian Stable Installation Notes

Debian Stable (Etch 4.0) installation notes

this is my first encounter with a Chado installation. Im using my old office machine.

• AMD Athlon(tm) XP 3200+
• 1 GB memory
• 500 GB SATA disk

I borrowed a lot of stuff from the Installing_Chado_on_Ubuntu_HOWTO page as Debian and Ubuntu are much alike.

Apache

Apache 2.2 is installed by default during the installation of Debian stable (web package).

location for GMOD

mkdir /usr/local/gmod

note: this is NOT the home of my gmod user.

download

got the source from sourceforge and unpacked in /usr/local/gmod (maybe I should use the cvs version??)

postgresql setup

Note: Debian stable has postgresql 7.4 as default package, but i'm going for 8.1.11 as this is also the version that runs on our RedHat Enterprise 5 server (more on that later)

apt-get install the following packages, Synaptic is your friend

• postgresql-8.1
• postgresql-8.1-client-common
• postgresql-client-8.1
• postgresql-contrib-8.1
• postgresql-plperl-8.1

Not necessary, but I also installed phpPgAdmin from source, not the Debian package.

Following the guidelines from INSTALL.Chado to add a database user and optimize some settings. Don't forget to create a database user root as well for the CPAN installations below, otherwise some tests fail. I added user 'chado' for the chado database installation.

The configuration files are located in a different location as opposed to our Redhat installation:

/etc/postgresql/8.1/main

I opted to install the CPAN modules instead of the Debian packages as some of the Debian packages have older versions of the modules. The modules are installed in

/usr/local/share/perl/5.8.8/

So not overwriting any installed Debian packages.

CPAN packages

CGI
GD
DBI
DBD::Pg
SQL::Translator
Digest::MD5
Text::Shellwords
Graph
Data::Stag
XML::Parser::PerlSAX
Module::Build
Class::DBI
Class::DBI::Pg
Class::DBI::Pager
DBIx::DBStag (Force install needed)
XML::Simple
LWP
Template
Log::Log4perl
GO::Parser

BioPerl

I installed BioPerl-live using subversion into /usr/local/bioperl/bioperl-live (as root)

svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk bioperl-live

cd /usrlocal/bioperl/bioperl-live
perl Build.PL
./Build
./Build test   #some tests fail as usual
sudo ./Build install

Environment Variables

Added this to my .bashrc so that when I login as user gmod all vars are set

# GMOD additions
export GMOD_ROOT=/usr/local/gmod
export GO_ROOT=/usr/local/share/perl/5.8.8/GO/
export PERL5LIB=$PERL5LIB:/usr/local/bioperl/bioperl-live
export CHADO_DB_NAME=dev_chado_01
export CHADO_DB_USERNAME=chado
export CHADO_DB_PASSWORD=******
#CHADO_DB_HOST=localhost
#CHADO_DB_PORT=5432

=== installing Chado scheme and tools

in /usr/local/gmod
perl Makefile.PL

make
sudo make install
make load_schema
make prepdb

a quick look at the database user phpPgAdmin: the database looks fine.

make ontologies
 ./Build ontologies
 Available ontologies:
 [1] Relationship Ontology
 [2] Sequence Ontology
 [3] Gene Ontology
 [4] Chado Feature Properties
 [5] Cell Ontology
 [6] Plant Ontology

 Which ontologies would you like to load (Comma delimited)? [0] 1,2,3,4

This take a while. i'm getting the notorious duplicate key violates unique constraint "cvterm_c1" error as well.