From: Naama M. <naa...@gm...> - 2017-04-12 17:46:20
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hi Mara, where did you install Bio::GMOD ? If that directory is not in @INC then you need to add it to your $PERL5LIB -Naama On Wed, Apr 12, 2017 at 1:30 PM Mara Kim <mar...@gm...> wrote: > Hi Naama, > > I am trying to use the gmod_load_cvterms.pl script, but I get the > following error: > > $ perl gmod_load_cvterms.pl -H localhost -D genestation > /raid/chado/ontology/ff-phase2-140729.obo > > Can't locate Bio/GMOD/Config.pm in @INC (@INC contains: > /home/kimmm/perl5/lib/perl5/5.10.1/x86_64-linux-thread-multi > /home/kimmm/perl5/lib/perl5/5.10.1 > /home/kimmm/perl5/lib/perl5/x86_64-linux-thread-multi > /home/kimmm/perl5/lib/perl5/5.10.0 /home/kimmm/perl5/lib/perl5 > /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl > /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at > gmod_load_cvterms.pl line 155. > > BEGIN failed--compilation aborted at gmod_load_cvterms.pl line 155. > > > I have Bio::GMOD installed. Are there other dependencies that I am > missing? > > On Mon, Mar 27, 2017 at 12:21 PM Naama Menda <naa...@gm...> > wrote: > > hi Mara, > > you could try to use the gmod_load_cvterms.pl > <https://github.com/GMOD/Chado/blob/master/chado/bin/gmod_load_cvterms.pl> > script > It should handle updating an existing ontology > > > -Naama > > > -- > > On Mon, Mar 27, 2017 at 1:16 PM Mara Kim <mar...@gm...> wrote: > > I temporarily renamed my `chado` schema to `public`. Now I am getting a > different error: > > $ stag-storenode.pl -d > 'dbi:Pg:dbname=genestation;host=localhost;port=5432' --user rokaschado > ff.xml > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > DBD::Pg::st execute failed: ERROR: duplicate key value violates unique > constraint "cvterm_c1" > > DETAIL: Key (name, cv_id, is_obsolete)=(myoblast, 121, 0) already > exists. [for Statement "INSERT INTO cvterm (dbxref_id, cv_id, name) VALUES > (?, ?, ?)" with ParamValues: 1='166192983', 2='121', 3='myoblast'] at > /home/kimmm/perl5/lib/perl5/DBIx/DBStag.pm line 3322. > > > I am guessing this is because I am loading the Fantom5 ontology, which > references terms from the UBERON ontology. I have already loaded the > UBERON ontology and am using it extensively. Is stag-storenode unable to > resolve this by not recreating duplicated terms? > > On Fri, Mar 24, 2017 at 11:53 AM Karl O. Pinc <ko...@me...> wrote: > > Hi, > > When we installed chado we found a number of places > where "public" was hardcoded. > > The places I identify now from a quick review of our notes are: > > initialize.sql > /usr/local/share/perl5/DBIx/DBSchema/DBD/Pg.pm > ---------------------<snip>-------------------- > --- Pg.pm~ 2014-04-01 10:43:28.916334643 -0400 > +++ Pg.pm 2014-04-21 12:02:33.960290072 -0400 > @@ -34,7 +34,8 @@ > > =cut > > -sub default_db_schema { 'public'; } > +#sub default_db_schema { 'public'; } > +sub default_db_schema { 'chado'; } > > sub columns { > my($proto, $dbh, $table) = @_; > ---------------------<snip>-------------------- > > I recall getting chado to install somewhere other than the public > schema to be tedious. > > Regards, > > Karl <ko...@me...> > Free Software: "You don't pay back, you pay forward." > -- Robert A. Heinlein > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > > |