Zheng's installation notes

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[edit] general information

There suppose to be an easy way and a hard way to install Chado database on Fedora:

  • the easy way: use an existing rpm package. I have not tried it. but you can find information at installation using an RPM
  • the hard way: install by source. But yum makes it easier. The following is my note on installation of Chado on Fedora 6.

[edit] before you start

[edit] get chado schema from cvs

see Chado From CVS, issue cvs command at my home directory.

[edit] install prerequisites

[edit] install Ant

sudo yum install ant

[edit] install postgresql

  • install both client and server by yum 
[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)

  • make server run 
[zha@localhost ~] sudo /sbin/service postgres start

to make it run at boot 

[zha@localhost ~] sudo /sbin/chkconfig postgres on
  • in .bash_profile add line 
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"?
  • create PL language, template, several roles 
[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.

  • edit the pg_hba.conf

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)

  • tune the server

haven't done yet.

[edit] install several general perl modules

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)

[edit] install bioperl live

[zha@localhost ~]$ sudo cpan
Password:
cpan[1]> install S/SE/SENDU/bioperl-1.5.2_102

this is the live bioperl right now

[edit] install go-dev

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.

  • in .bash_profile add line 
export GO_ROOT="$HOME/go-dev"
  • install GO::Parser 
[zha@localhost ~]$ sudo cpan
Password:
cpan[1]> install GO::Parser

[edit] install chado

  • in .bash_profile add lines 
export GMOD_ROOT="/usr/local/gmod"
export CHADO_DB_NAME="yeast_chado"
export CHADO_DB_USERNAME="zha"
  • standard perl package install 
perl Makefile.PL
make
sudo make install

and then: 

make load_schema
make prepdb
make ontologies
  • backup ontologies 
pg_dump wormbase_chado > onto_only.sql
  • load sample yeast genome data

download yeast genome gff3 file. load by bulk load 

gmod_bulk_load_gff3.pl --organism yeast --gfffile saccharomyces_cerevisiae.gff

[edit] install gbrowse to work with chado

  • install gbrowse

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
  • work with chado

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 (?)

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