Zheng's installation notes

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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.

before you start

get chado schema from cvs

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

install prerequisites

install Ant

sudo yum install ant

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.

local   all         all                               trust
host    all         all          trust
host    all         all         ::1/128               trust

need revisit for local access and access method (MD5)

  • tune the server

haven't done yet.

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)

install bioperl live

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

this is the live bioperl right now

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
cpan[1]> install GO::Parser

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
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

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
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 (?)