Difference between revisions of "Zheng's installation notes"

Revision as of 22:30, 19 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 yum installed in your path;
• you have cpan installed in your path;
• you have cvs installed in your path;
• 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.
• make server run
• create PL language, template, several roles
• edit the pg_hba.conf
• tune the server

install bioperl live

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

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