Difference between revisions of "Zheng's installation notes"

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(install [http://www.postgresql.org/ postgresql])
(install [http://search.cpan.org/~sendu/bioperl-1.5.2_102/ bioperl live])
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  Password:
 
  Password:
 
  cpan[1]> install S/SE/SENDU/bioperl-1.5.2_102
 
  cpan[1]> install S/SE/SENDU/bioperl-1.5.2_102
 +
this is the live bioperl right now
  
 
===install [http://sourceforge.net/projects/geneontology go-dev]===
 
===install [http://sourceforge.net/projects/geneontology go-dev]===

Revision as of 15:31, 20 March 2007

Back to Chado New Users

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 postgresql

  • install both client and server by yum
[zha@localhost ~] sudo yum install postgresql
[zha@localhost ~] sudo yum install postgresql-server
  • make server run
[zha@localhost ~] sudo /sbin/service postgres start

to make it run at boot

[zha@localhost ~] sudo /sbin/chkconfig postgres on
  • create PL language, template, several roles
[zha@localhost ~] creatlang 
  • 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

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