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 2.2 is installed by default during the installation of Debian stable (web package).
location for GMOD
note: this is NOT the home of my gmod user.
got the source from sourceforge and unpacked in /usr/local/gmod (maybe I should use the cvs version??)
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
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:
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
So not overwriting any installed Debian 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
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
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:  Relationship Ontology  Sequence Ontology  Gene Ontology  Chado Feature Properties  Cell Ontology  Plant Ontology
Which ontologies would you like to load (Comma delimited)?  1,2,3,4
This take a while. i'm getting the notorious duplicate key violates unique constraint "cvterm_c1" error as well.