Difference between revisions of "Installing Chado on Ubuntu HOWTO"

Revision as of 14:17, 6 September 2012

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Ubuntu version

This was originally written for Ubuntu 8.4 and PostgreSQL 8.1 and updated for Ubuntu 11.10 and PostgreSQL 9.1. Note also that starting with the 12.10 Ubuntu release (in October, 2012), this will get even easier, since there will be a Debian package for Chado available (libchado-perl) that will make installation a real snap. That packages is already available for Debian installations.

Notes

Installing prereqs with Synaptic:

• postgresql
• postgresql-client
• postgresql-contrib
• postgresql-plperl
• libpq-dev
• libdbd-pg-perl
• libtemplate-perl -- Template toolkit
• libxml-simple-perl
• liblog-log4perl-perl
• ant
• libparse-recdescent-perl # needed by DBIx::DBStag
• xsltproc
• bioperl

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

Created a db user for me:

 $ sudo su - postgres
 $ createuser scott
 Shall the new role be a superuser? (y/n) y
 CREATE ROLE
 $ 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 scott with password 'mypassword';
 $ exit #from psql
 $ exit #from sudo

Installing prereqs with cpan shell:

• install Bio::Chado::Schema
• install GO::Parser (go-perl)
• install DBIx::DBSchema # needed by DBIx::DBStag

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.)

 wget http://search.cpan.org/CPAN/authors/id/C/CM/CMUNGALL/DBIx-DBStag-0.10.tar.gz
 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
 make test  #all tests pass
 sudo make install

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

 export GMOD_ROOT=/usr/local/gmod
 export CHADO_DB_NAME=chado
 export CHADO_DB_USER=scott
 export CHADO_DB_PASS=mypassword
 export CHADO_DB_HOST=localhost
 export CHADO_DB_PORT=5432
 export GO_ROOT=/usr/local/share/perl/5.8.8/GO

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

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

Then, back in the gmod directory

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

Get and load yeast GFF3 file:

  wget ftp://ftp.yeastgenome.org/sequence/S288C_reference/genome_release/S288C_reference_genome_Current_Release.tgz

  gmod_bulk_load_gff3.pl -g saccharomyces_cerevisiae.gff

• Note that I had to install the perl module "version::vxs" for some reason--it is not a prerequisite for any GMOD software, but must be an undeclared prereq for something that GMOD software depends on. Hopefully this will be fixed by the author soon.