Difference between revisions of "Installing Chado on Ubuntu HOWTO"
From GMOD
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Get and load yeast [[GFF3]] file: | Get and load yeast [[GFF3]] file: | ||
− | wget ftp://ftp.yeastgenome.org/ | + | wget ftp://ftp.yeastgenome.org/sequence/S288C_reference/genome_release/S288C_reference_genome_Current_Release.tgz |
− | + | ||
− | + | ||
gmod_bulk_load_gff3.pl -g saccharomyces_cerevisiae.gff | gmod_bulk_load_gff3.pl -g saccharomyces_cerevisiae.gff | ||
+ | |||
+ | *Note that I had to install the perl module "version::vxs" for some reason--it is not a prerequisite for any GMOD software, but must be an undeclared prereq for something that GMOD software depends on. Hopefully this will be fixed by the author soon. | ||
[[Category:HOWTO]] | [[Category:HOWTO]] | ||
[[Category:Chado]] | [[Category:Chado]] | ||
[[Category:Linux]] | [[Category:Linux]] |
Revision as of 01:47, 15 March 2012
Ubuntu version
This was originally written for Ubuntu 8.4 and PostgreSQL 8.1 and updated for Ubuntu 11.10 and PostgreSQL 9.1.
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
- xsltproc
- bioperl
sudo apt-get install postgresql postgresql-client postgresql-contrib postgresql-plperl libpq-dev libdbd-pg-perl libtemplate-perl libxml-simple-perl liblog-log4perl-perl ant libparse-recdescent-perl xsltproc bioperl
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/9.1/main/pg_hba.conf #changed "local all all" and "host all all" lines from ident sameuser to trust $ exit $ sudo /etc/init.d/postgresql 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 Bio::Chado::Schema
- install GO::Parser (go-perl)
- install DBIx::DBSchema # needed by DBIx::DBStag
Installed DBIx::DBStag 'by hand':
(Note that if you have the cpan shell set up to do "sudo make" rather than running the whole shell as root (via "sudo cpan"), you can install DBIx::DBStag from the cpan shell.)
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
Get and load yeast GFF3 file:
wget ftp://ftp.yeastgenome.org/sequence/S288C_reference/genome_release/S288C_reference_genome_Current_Release.tgz
gmod_bulk_load_gff3.pl -g saccharomyces_cerevisiae.gff
- Note that I had to install the perl module "version::vxs" for some reason--it is not a prerequisite for any GMOD software, but must be an undeclared prereq for something that GMOD software depends on. Hopefully this will be fixed by the author soon.