This is the new server for GMOD.org. Please let us know if you notice anything weird while it's getting broken in.
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 (?)