From: Naama M. <naa...@gm...> - 2017-04-18 00:15:51
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hi Mara, yes, this is a command line arg. It requires a number of arguments, it's listed in the perldoc. This script loads one ontology at a time, so it expects all terms to have one prefix If you have more than one and also references to other ontologies, you might hit some more roadblocks Can you send me the obo for the ontology you are trying to load? I could see if I could make some changes to make this script compatible with it best, -Naama On Mon, Apr 17, 2017 at 4:45 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 >>> >>> |