Difference between revisions of "Installing Chado on Ubuntu HOWTO"
From GMOD
Line 73: | Line 73: | ||
./Build test #a few tests fail, but that's ok | ./Build test #a few tests fail, but that's ok | ||
sudo ./Build install | 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 |
Revision as of 17:10, 13 November 2007
Notes
Installing prereqs with Syanptic:
- 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
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/8.2/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:
- install CMUNGALL/go-perl-0.07.tar.gz
- install DBIx::DBSchema # needed by DBIx::DBStag
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-0.09.tar.gz cd DBIx-DBStag-0.09 createdb test # needed for the make test step make make test #some (but not most) tests failed, installing anyway 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= 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
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