From: Mara K. <mar...@gm...> - 2017-04-17 21:01:08
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This is further complicated by the fact that the ids use multiple db.names On Mon, Apr 17, 2017 at 3:44 PM Mara Kim <mar...@gm...> wrote: > Ok, so I think I have fixed the previous errors. Now I am getting this > message: > > $ perl gmod_load_cvterms.pl -H localhost -D genestation > /raid/chado/ontology/ff-phase2-140729.obo > > Need -s db.name argument! (e.g. GO , PO, etc. > > at gmod_load_cvterms.pl line 180. > > > Is this asking for a command line argument? I'm not sure what the proper > value should be because this ontology spans / includes terms from many > existing ontologies. > > On Wed, Apr 12, 2017 at 9:01 PM Naama Menda <naa...@gm...> wrote: > >> >> Config.pm is in the GMOD git repo (and not in Bio::GMOD that you get >> from CPAN) >> https://github.com/GMOD/Chado/tree/master/chado/lib/Bio/GMOD >> >> you should have the chado scripts in a chado/bin directory, and the >> Bio::GMOD modules in chado/lib/GMOD... >> then add the path for chado/lib to your $PERL5LIB >> >> >> -Naama >> >> >> >> >> >> On Wed, Apr 12, 2017 at 2:23 PM Mara Kim <mar...@gm...> wrote: >> >>> Ok, so I checked the location of my Bio::GMOD and I noticed that there >>> is no subfolder `Config` which the script seems to be looking for: >>> >>> $ ls /home/kimmm/perl5/lib/perl5/Bio/GMOD >>> >>> *Adaptor* Adaptor.pm *Admin* *Query* Query.pm StandardURLs.pm >>> *Util* >>> >>> >>> Am I missing something? I have version 0.028 installed using cpanm. >>> >>> On Wed, Apr 12, 2017 at 12:46 PM Naama Menda <naa...@gm...> >>> wrote: >>> >>> 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 >>> >>> |