Difference between revisions of "Installing Chado on Ubuntu HOWTO"

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(adding a package dependency)
Line 7: Line 7:
 
*postgresql-contrib
 
*postgresql-contrib
 
*postgresql-plperl
 
*postgresql-plperl
 +
*libpq-dev
 
*libdbd-pg-perl
 
*libdbd-pg-perl
 
*libtemplate-perl -- Template toolkit
 
*libtemplate-perl -- Template toolkit
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If you are using postgres 8.3 (which is the default on Ubuntu Hardy July 31 2008),
 
If you are using postgres 8.3 (which is the default on Ubuntu Hardy July 31 2008),
 
<pre>
 
<pre>
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
+
sudo apt-get install postgresql postgresql-client postgresql-contrib postgresql-plperl-8.3 libpq-dev libdbd-pg-perl libtemplate-perl libxml-simple-perl liblog-log4perl-perl ant libparse-recdescent-perl
 
</pre>
 
</pre>
 
Otherwise change the postgresql-plperl-8.3 to suit.
 
Otherwise change the postgresql-plperl-8.3 to suit.

Revision as of 18:00, 11 October 2011

Notes

Installing prereqs with Synaptic:

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

If you are using postgres 8.3 (which is the default on Ubuntu Hardy July 31 2008),

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

Otherwise change the postgresql-plperl-8.3 to suit.

Created a db user for me:

 $ sudo su - postgres
 $ createuser scott
 Shall the new role be a superuser? (y/n) y
 CREATE ROLE
 $ vi /etc/postgresql/8.3/main/pg_hba.conf
 #changed "local all all" and "host all all" lines from ident sameuser to trust
 $ exit
 $ sudo /etc/init.d/postgresql-8.3 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 scott with password 'mypassword';
 $ 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


Installed DBIx::DBStag 'by hand':

 wget http://search.cpan.org/CPAN/authors/id/C/CM/CMUNGALL/DBIx-DBStag-0.10.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=scott
 export CHADO_DB_PASS=mypassword
 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

Installed bioperl-live from cvs:

 wget http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/bioperl-live/bioperl-live.tar.gz?tarball=1&cvsroot=bioperl
 tar zxvf bioperl-live.tar.gz
 cd bioperl-live
 perl Build.PL
 ./Build
 ./Build test   #a few tests fail, but that's ok
 sudo ./Build install

Get and load yeast GFF3 file:

  wget ftp://ftp.yeastgenome.org/yeast/chromosomal_feature/saccharomyces_cerevisiae.gff
  #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