From: Mara K. <mar...@gm...> - 2017-04-17 20:45:15
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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 >> >> |