Difference between revisions of "Zheng's installation notes"
From GMOD
(→install [http://www.postgresql.org/ postgresql]) |
(→install [http://www.postgresql.org/ postgresql]) |
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*in .bash_profile add line | *in .bash_profile add line | ||
export PGDATA="/var/lib/pgsql/data/" | export PGDATA="/var/lib/pgsql/data/" | ||
− | But I still can't get rid of the -D /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 | [zha@localhost gff3]$ sudo -u postgres postgres | ||
postgres does not know where to find the server configuration file. | postgres does not know where to find the server configuration file. |
Revision as of 15:49, 20 March 2007
Back to Chado New Users
Contents
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
- 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