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Installing Chado on Ubuntu HOWTO
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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.