Difference between revisions of "Zheng's installation notes"

Revision as of 16:20, 20 March 2007

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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

• you can be a superuser or you can sudo to install packages;
• you have read the chado INSTALL document

get chado schema from cvs

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

install prerequisites

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.

[zha@localhost ~] sudo -u postgres createuser root

this must be a superuser of postgresql (same privilege as postgres)

• 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

install several general perl modules

use sudo cpan to do it. install CGI Graph

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

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