Difference between revisions of "Zheng's installation notes"
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*backup ontologies | *backup ontologies | ||
pg_dump wormbase_chado > onto_only.sql | pg_dump wormbase_chado > onto_only.sql | ||
+ | *load sample yeast genome data | ||
+ | download yeast genome gff3 file at ftp://ftp.yeastgenome.org/pub/yeast/data_download/chromosomal_feature/saccharomyces_cerevisiae.gff | ||
+ | gmod_bulk_load_gff3.pl --organism yeast --gfffile saccharomyces_cerevisiae.gff | ||
==install gbrowse to work with chado== | ==install gbrowse to work with chado== |
Revision as of 18:07, 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. 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.
# 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
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)
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 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
install chado
- in .bash_profile add lines
export GMOD_ROOT="/usr/local/gmod" export CHADO_DB_NAME="wormbase_chado" export CHADO_DB_USERNAME="zha"
- standard perl package install
perl Makefile.PL make sudo make install 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 at ftp://ftp.yeastgenome.org/pub/yeast/data_download/chromosomal_feature/saccharomyces_cerevisiae.gff
gmod_bulk_load_gff3.pl --organism yeast --gfffile saccharomyces_cerevisiae.gff