Back to Chado New Users
There suppose to be an easy way and a hard way to install Chado database on Fedora:
see Chado From CVS, issue cvs command at my home directory.
rel=”nofollow”>Ant</a></span>
sudo yum install ant
rel=”nofollow”>postgresql</a></span>
[zha@localhost ~] sudo yum install postgresql
[zha@localhost ~] sudo yum install postgresql-server
right now the version is 8.1.8 (in yum package pool)
[zha@localhost ~] sudo /sbin/service postgres start
to make it run at boot
[zha@localhost ~] sudo /sbin/chkconfig postgres on
export PGDATA="/var/lib/pgsql/data/"
But I still can’t get rid of the -D /var/lib/pgsql/data/ why???
[zha@localhost gff3]$ sudo -u postgres postgres
postgres does not know where to find the server configuration file.
You must specify the --config-file or -D invocation option or set the PGDATA environment variable.
[zha@localhost gff3]$ sudo -u postgres postgres -D /var/lib/pgsql/data
FATAL: lock file "postmaster.pid" already exists
HINT: Is another postmaster (PID 2785) running in data directory "/var/lib/pgsql/data"?
[zha@localhost ~] sudo -u postgres creatlang plpgsql template1
[zha@localhost ~] sudo -u postgres createuser zha
replace zha with your own account name at your home directory. this must be a user with privilege to create and drop database. this is purely for the purpose of smooth installation.
[zha@localhost ~] sudo -u postgres createuser root
this must be a superuser of postgresql (same privilege as postgres), this is for installing DBIx::DBStag.
the pg_hba.conf is in /var/lib/pgsql/data/pg_hba.conf, you probably need to chown to postgres.
# TYPE DATABASE USER CIDR-ADDRESS METHOD
local all all trust
host all all 127.0.0.1/32 trust
host all all ::1/128 trust
need revisit for local access and access method (MD5)
haven’t done yet.
use sudo cpan to do it. install
CGI (GBrowse)
GD (GBrowse)
DBI (GBrowse,chado)
DBD::Pg (1.49 or better) (GBrowse,chado)
you can also install it by
yum install perl-DBD-Pg
Digest::MD5 (GBrowse)
Text::Shellwords (GBrowse)
Data::Stag (chado)
XML::Parser::PerlSAX (chado)
Module::Build (chado)
Class::DBI (GMODWeb, or with a custom Chado schema)
Class::DBI::Pg (GMODWeb, or with a custom Chado schema)
Class::DBI::Pager (GMODWeb, or with a custom Chado schema)
DBIx::DBStag (chado)
XML::Simple (chado)
LWP (chado)
Template (chado)
Log::Log4perl (chado)
Term::ProgressBar (2.06 or better) (chado)
class=”external text” rel=”nofollow”>bioperl live</a></span>
[zha@localhost ~]$ sudo cpan
Password:
cpan[1]> install S/SE/SENDU/bioperl-1.5.2_102
this is the live bioperl right now
class=”external text” rel=”nofollow”>go-dev</a></span>
download and unpack the go-dev package since need to set the GO_ROOT environment variable. Although right now only a perl parser module for GO is needed.
export GO_ROOT="$HOME/go-dev"
[zha@localhost ~]$ sudo cpan
Password:
cpan[1]> install GO::Parser
export GMOD_ROOT="/usr/local/gmod"
export CHADO_DB_NAME="yeast_chado"
export CHADO_DB_USERNAME="zha"
perl Makefile.PL
make
sudo make install
and then:
make load_schema
make prepdb
make ontologies
pg_dump wormbase_chado > onto_only.sql
download yeast genome gff3 file. load by bulk load
gmod_bulk_load_gff3.pl --organism yeast --gfffile saccharomyces_cerevisiae.gff
download Gbrowse, unpack it. standard install procedure. But be sure to read README.fedora and disable SELINUX for apache!!!
perl Makefile.PL HTDOCS=/var/www/html CONF=/etc/httpd/conf CGIBIN=/var/www/cgi-bin --SELINUX=1
make
sudo make install UNINST=1
who is running apache?
[zha@localhost ~]$ ps -ef |grep httpd
in my machine it is ‘apache’. configure gbrowse to work with chado.
cp /home/zha/Generic-Genome-Browser-1.67/contrib/conf_files/07.chado.conf /etc/httpd/conf/gbrowse.conf/yeast_chado.conf
make two-line-change to yeast_chado.conf
database = dbi:Pg:dbname=yeast_chado;host=localhost;port=5432
user = apache
grant select privilege on several tables to apache
grant select on feature to apache;
in Mac it is www, see Jim’s installation notes.
it is a little bit surprise to me that I need
grant select on analysisfeature to apache;
since no analysisfeature exists in dataset (?)