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View Chado Installation

Instalacion de Chado en Ubuntu

Primero se deben instalar las siguietes librerias en ubuntu que son prerequisitos para la instalacion de chado

aptitude install libgd2 libmysqlclient-dev libdbd-mysql-perl FastCGI libmysqlclient16 libgd2-dev libgd2-xpm-dev libarchive-zip-perl libarchive-tar-perl ncftp mod_perl libc6-dev postgresql-server-dev-8.3 wget cvs subversion build-essential libpng12-dev libgd-gd2-perl libmodule-build-perl libio-string-perl libcgi-session-perl libwww-perl libstatistics-descriptive-perl libjson-perl libjson-any-perl libdbd-pg-perl libapache2-mod-perl2 libapache2-mod-fastcgi libapache2-mod-fcgid libfcgi-perl inkscape libsvg-perl perl-doc libgdl-1-3 libgdl-1-common libgdl-1-dbg libgdl-1-dev

A continuacion se instalas los siguietes modulos a traves del cpan

perl -MCPAN -e shell

install Bundle::CPAN

install Module::Build

install GD

install Data::Stag

o conf prefer_installer MB

o conf commit

q

perl -MCPAN -e shell

install DBIx::DBSchema install Parse::RecDescent install XML::Parser::PerlSAX

Instalar otros prerequisitos con synaptic:

* postgresql * postgresql-client * postgresql-contrib * postgresql-plperl * libdbd-pg-perl * libtemplate-perl — Template toolkit * libxml-simple-perl * liblog-log4perl-perl * ant * libparse-recdescent-perl # needed by DBIx::DBStag

sudo apt-get install postgresql postgresql-client postgresql-contrib postgresql-plperl-8.3 libdbd-pg-perl libtemplate-perl libxml-simple-perl liblog-log4perl-perl ant libparse-recdescent-perl

Crear un usario de base de datos para el usuario de ubuntu: $ sudo su – postgres $ createuser william Shall the new role be a superuser? (y/n) y CREATE ROLE $ createuser root Shall the new role be a superuser? (y/n) y CREATE ROLE

$ vi /etc/postgresql/8.3/main/pg_hba.conf

1. changed “local all all” and “host all all” lines from ident sameuser to trust

$ exit $ sudo /etc/init.d/postgresql-8.3 restart

It is useful to actually have a password, even using trust, otherwise problems with DBD::Pg pop up telling you that no password was supplied.

$ sudo su – postgres

$ psql -d template1

$ alter USER william with password ‘xxxxxx’;

$ alter USER root with password ‘xxxxxx’;

$ exit #from psql

$ exit #from sudo

Installing prereqs with cpan shell:

* install CMUNGALL/go-perl-0.09.tar.gz * install DBIx::DBSchema # needed by DBIx::DBStag * install Module::Build # needed by GMOD Makefile.PL * install DBD::Pg #required by GMOD make ontologies

install Bundle::GMOD

Si instala los prerequisitos de GMOD bien no es necesario de hacer lo siguiente Installed DBIx::DBStag ‘by hand’: wget http://search.cpan.org/CPAN/authors/id/C/CM/CMUNGALL/DBIx-DBStag-0.09.tar.gz tar zxvf DBIx-DBStag-0.10.tar.gz cd DBIx-DBStag-0.10 createdb test # needed for the make test step perl Makefile.PL make make test #all tests pass sudo make install

Created the file ~/.gmod_profile, with the contents:

export GMOD_ROOT=/usr/local/gmod

export CHADO_DB_NAME=chado

export CHADO_DB_USER=william

export CHADO_DB_PASS=xxxxxx

export CHADO_DB_HOST=localhost

export CHADO_DB_PORT=5432

export GO_ROOT=/usr/local/share/perl/5.8.8/GO

and added this line to the end of ~/.bash_profile:

. ~/.gmod_profile #sources the gmod profile on login

Then, back in the gmod directory perl Makefile.PL make sudo make install make load_schema make prepdb make ontologies #selected 1,2,3,4

Instalar bioPerl desde los fuentes con todas las opciones por defecto Instalar io_lib-1.12.2 desde los funtes Instalar Bio-SCF desde los fuentes

sudo perl -MCPAN -e shell

Get and load yeast GFF3 file: wget ftp://ftp.yeastgenome.org/yeast/chromosomal_feature/saccharomyces_cerevisiae.gff

1. fix the obsolete SO term in the GFF file:

perl -pi -e ‘s/\trepeat_family\t/\trepeat_region\t/’ saccharomyces_cerevisiae.gff gmod_bulk_load_gff3.pl -g saccharomyces_cerevisiae.gff

cp /home/zha/Generic-Genome-Browser-1.67/contrib/conf_files/07.chado.conf /etc/httpd/conf/gbrowse.conf/yeast_chado.conf

modify yeast_chado.conf

db_adaptor = Bio::DB::Das::Chado database = dbi:Pg:dbname=chado;host=localhost;port=5432;user=william;password=xxxxxx