Installing Chado on Ubuntu HOWTO

Notes

Installing prereqs with Synaptic:

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

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/8.2/main/pg_hba.conf
 #changed "local all all" and "host all all" lines from ident sameuser to trust 
 $ exit
 $ sudo /etc/init.d/postgresql-8.2 restart

Installing prereqs with cpan shell:

• install CMUNGALL/go-perl-0.07.tar.gz
• install DBIx::DBSchema # needed by DBIx::DBStag

Installed DBIx::DBStag 'by hand':

 wget http://search.cpan.org/CPAN/authors/id/C/CM/CMUNGALL/DBIx-DBStag-0.09.tar.gz
 tar zxvf DBIx-DBStag-0.09.tar.gz
 cd DBIx-DBStag-0.09
 createdb test   # needed for the make test step
 make
 make test  #some (but not most) tests failed, installing anyway
 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=
 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

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

Installed bioperl-live from cvs:

 wget http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/bioperl-live.tar.gz?tarball=1&cvsroot=bioperl
 tar zxvf bioperl-live.tar.gz
 cd bioperl-live
 perl Build.PL
 ./Build
 ./Build test   #a few tests fail, but that's ok
 sudo ./Build install

Get and load yeast GFF3 file:

  wget ftp://ftp.yeastgenome.org/yeast/chromosomal_feature/saccharomyces_cerevisiae.gff
  #fix the obsolete SO term in the GFF file:
   perl -pi -e 's/\trepeat_family\t/\trepeat_region\t/' saccharomyces_cerevisiae.gff
  gmod_bulk_load_gff3.pl -g saccharomyces_cerevisiae.gff