Difference between revisions of "Debian Stable Installation Notes"

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m (New page: These*liblog-log4perl-perl *ant *libparse-recdescent-perl # needed by DBIx::DBStag Created a db user for me: $ sudo su - postgres $ createuser scott Shall the new role be a superu...)
 
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These*liblog-log4perl-perl
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==Debian Stable (Etch 4.0) installation notes==
−
*ant
+
−
*libparse-recdescent-perl  # needed by DBIx::DBStag
+
  
−
Created a db user for me:
+
this is my first encounter with a Chado installation. Im using my old office machine.
 +
* AMD Athlon(tm) XP  3200+
 +
* 1 GB memory
 +
* 500 GB SATA disk
  
−
  $ sudo su - postgres
+
I borrowed a lot of stuff from the [[Installing_Chado_on_Ubuntu_HOWTO]] page as Debian and Ubuntu are much alike.
−
  $ createuser scott
+
=== Apache ===
−
  Shall the new role be a superuser? (y/n) y
+
Apache 2.2 is installed by default during the installation of Debian stable (web package).
−
  CREATE ROLE
+
−
  $ vi /etc/postgresql/8.2/main/pg_hba.conf
+
−
  #changed "local all all" and "host all all" lines from ident sameuser to trust
+
−
  $ exit
+
−
  $ sudo /etc/init.d/postgresql-8.2 restart
+
  
−
Installing prereqs with cpan shell:
+
=== location for GMOD ===
 +
mkdir /usr/local/gmod
 +
note: this is NOT the home of my gmod user.
  
−
*install CMUNGALL/go-perl-0.07.tar.gz
+
=== download ===
 +
got the source from [http://sourceforge.net/project/showfiles.php?group_id=27707&package_id=19511 sourceforge] and unpacked in /usr/local/gmod
 +
(maybe I should use the cvs version??)
 +
 
 +
=== postgresql setup ===
 +
Note: Debian stable has postgresql 7.4 as default package, but i'm going for 8.1.11 as this is also the version that runs on our RedHat Enterprise 5 server (more on that later)
 +
 
 +
apt-get install the following packages, Synaptic is your friend
 +
 
 +
* postgresql-8.1
 +
* postgresql-8.1-client-common
 +
* postgresql-client-8.1
 +
* postgresql-contrib-8.1
 +
* postgresql-plperl-8.1
 +
 
 +
Not necessary, but I also installed phpPgAdmin from source, not the Debian package.
 +
 
 +
Following the guidelines from INSTALL.Chado to add a database user and optimize some settings. Don't forget to create a database user root as well for the CPAN installations below, otherwise some tests fail. I added user 'chado' for the chado database installation.
 +
 
 +
The configuration files are located in a different location as opposed to our Redhat installation:
 +
 +
/etc/postgresql/8.1/main
 +
 
 +
 
 +
I opted to install the CPAN modules instead of the Debian packages as some of the Debian packages have older versions of the modules. The modules are installed in
 +
 
 +
/usr/local/share/perl/5.8.8/
 +
 
 +
So not overwriting any installed Debian packages.
 +
 
 +
==== CPAN packages ====
 +
CGI
 +
GD
 +
DBI
 +
DBD::Pg
 +
SQL::Translator
 +
Digest::MD5
 +
Text::Shellwords
 +
Graph
 +
Data::Stag
 +
XML::Parser::PerlSAX
 +
Module::Build
 +
Class::DBI
 +
Class::DBI::Pg
 +
Class::DBI::Pager
 +
DBIx::DBStag (Force install needed)
 +
XML::Simple
 +
LWP
 +
Template
 +
Log::Log4perl
 +
GO::Parser
 +
 
 +
=== BioPerl ===
 +
I installed [http://www.bioperl.org/wiki/Using_Subversionon BioPerl-live ] using subversion into /usr/local/bioperl/bioperl-live (as root)
 +
 +
svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk bioperl-live
 +
 
 +
cd /usrlocal/bioperl/bioperl-live
 +
perl Build.PL
 +
./Build
 +
./Build test  #some tests fail as usual
 +
sudo ./Build install
 +
 
 +
 
 +
=== Environment Variables ===
 +
Added this to my .bashrc so that when I login as user gmod all vars are set
 +
# GMOD additions
 +
export GMOD_ROOT=/usr/local/gmod
 +
export GO_ROOT=/usr/local/share/perl/5.8.8/GO/
 +
export PERL5LIB=$PERL5LIB:/usr/local/bioperl/bioperl-live
 +
export CHADO_DB_NAME=dev_chado_01
 +
export CHADO_DB_USERNAME=chado
 +
export CHADO_DB_PASSWORD=******
 +
#CHADO_DB_HOST=localhost
 +
#CHADO_DB_PORT=5432
 +
 +
 
 +
=== installing Chado scheme and tools
 +
in /usr/local/gmod
 +
perl Makefile.PL
 +
 +
make
 +
sudo make install
 +
make load_schema
 +
make prepdb
 +
 
 +
a quick look at the database user phpPgAdmin: the database looks fine.
 +
 
 +
make ontologies
 +
  ./Build ontologies
 +
  Available ontologies:
 +
  [1] Relationship Ontology
 +
  [2] Sequence Ontology
 +
  [3] Gene Ontology
 +
  [4] Chado Feature Properties
 +
  [5] Cell Ontology
 +
  [6] Plant Ontology
 +
 
 +
  Which ontologies would you like to load (Comma delimited)? [0] 1,2,3,4
 +
 
 +
This take a while. i'm getting the notorious duplicate key violates unique constraint "cvterm_c1" error as well.
 +
 
 +
=== Data loading ===
 +
 
 +
[[Category:Packaging]]

Revision as of 10:08, 24 April 2008

Debian Stable (Etch 4.0) installation notes

this is my first encounter with a Chado installation. Im using my old office machine.

  • AMD Athlon(tm) XP 3200+
  • 1 GB memory
  • 500 GB SATA disk

I borrowed a lot of stuff from the Installing_Chado_on_Ubuntu_HOWTO page as Debian and Ubuntu are much alike.

Apache

Apache 2.2 is installed by default during the installation of Debian stable (web package).

location for GMOD

mkdir /usr/local/gmod

note: this is NOT the home of my gmod user.

download

got the source from sourceforge and unpacked in /usr/local/gmod (maybe I should use the cvs version??)

postgresql setup

Note: Debian stable has postgresql 7.4 as default package, but i'm going for 8.1.11 as this is also the version that runs on our RedHat Enterprise 5 server (more on that later)

apt-get install the following packages, Synaptic is your friend

  • postgresql-8.1
  • postgresql-8.1-client-common
  • postgresql-client-8.1
  • postgresql-contrib-8.1
  • postgresql-plperl-8.1

Not necessary, but I also installed phpPgAdmin from source, not the Debian package.

Following the guidelines from INSTALL.Chado to add a database user and optimize some settings. Don't forget to create a database user root as well for the CPAN installations below, otherwise some tests fail. I added user 'chado' for the chado database installation.

The configuration files are located in a different location as opposed to our Redhat installation: 

/etc/postgresql/8.1/main


I opted to install the CPAN modules instead of the Debian packages as some of the Debian packages have older versions of the modules. The modules are installed in 

/usr/local/share/perl/5.8.8/

So not overwriting any installed Debian packages.

CPAN packages

CGI
GD
DBI
DBD::Pg
SQL::Translator
Digest::MD5
Text::Shellwords
Graph
Data::Stag
XML::Parser::PerlSAX
Module::Build
Class::DBI
Class::DBI::Pg
Class::DBI::Pager
DBIx::DBStag (Force install needed)
XML::Simple
LWP
Template
Log::Log4perl
GO::Parser

BioPerl

I installed BioPerl-live using subversion into /usr/local/bioperl/bioperl-live (as root) 

svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk bioperl-live

cd /usrlocal/bioperl/bioperl-live
perl Build.PL
./Build
./Build test   #some tests fail as usual
sudo ./Build install


Environment Variables

Added this to my .bashrc so that when I login as user gmod all vars are set 

# GMOD additions
export GMOD_ROOT=/usr/local/gmod
export GO_ROOT=/usr/local/share/perl/5.8.8/GO/
export PERL5LIB=$PERL5LIB:/usr/local/bioperl/bioperl-live
export CHADO_DB_NAME=dev_chado_01
export CHADO_DB_USERNAME=chado
export CHADO_DB_PASSWORD=******
#CHADO_DB_HOST=localhost
#CHADO_DB_PORT=5432

=== installing Chado scheme and tools 

in /usr/local/gmod
perl Makefile.PL

make
sudo make install
make load_schema
make prepdb

a quick look at the database user phpPgAdmin: the database looks fine. 

make ontologies
 ./Build ontologies
 Available ontologies:
 [1] Relationship Ontology
 [2] Sequence Ontology
 [3] Gene Ontology
 [4] Chado Feature Properties
 [5] Cell Ontology
 [6] Plant Ontology

 Which ontologies would you like to load (Comma delimited)? [0] 1,2,3,4

This take a while. i'm getting the notorious duplicate key violates unique constraint "cvterm_c1" error as well.

Data loading

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