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Zheng's installation notes
Back to Chado New Users
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.
sudo yum install ant
- 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
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
DBD::Pg (1.49 or better) (GBrowse,chado)
you can also install it by
yum install perl-DBD-Pg
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)
Term::ProgressBar (2.06 or better) (chado)
install bioperl live
[zha@localhost ~]$ sudo cpan Password: cpan> install S/SE/SENDU/bioperl-1.5.2_102
this is the live bioperl right now
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
- install GO::Parser
[zha@localhost ~]$ sudo cpan Password: cpan> install GO::Parser
- in .bash_profile add lines
export GMOD_ROOT="/usr/local/gmod" export CHADO_DB_NAME="yeast_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. load by bulk load
gmod_bulk_load_gff3.pl --organism yeast --gfffile saccharomyces_cerevisiae.gff
install gbrowse to work with chado
- install gbrowse
download Gbrowse, unpack it. standard install procedure. But be sure to read README.fedora and disable SELINUX for apache!!!
perl Makefile.PL HTDOCS=/var/www/html CONF=/etc/httpd/conf CGIBIN=/var/www/cgi-bin --SELINUX=1 make sudo make install UNINST=1
- work with chado
who is running apache?
[zha@localhost ~]$ ps -ef |grep httpd
in my machine it is 'apache'. configure gbrowse to work with chado.
cp /home/zha/Generic-Genome-Browser-1.67/contrib/conf_files/07.chado.conf /etc/httpd/conf/gbrowse.conf/yeast_chado.conf
make two-line-change to yeast_chado.conf
database = dbi:Pg:dbname=yeast_chado;host=localhost;port=5432 user = apache
grant select privilege on several tables to apache
grant select on feature to apache;
in Mac it is www, see Jim's installation notes.
it is a little bit surprise to me that I need
grant select on analysisfeature to apache;
since no analysisfeature exists in dataset (?)