From: Mara K. <mar...@gm...> - 2017-04-19 00:17:40
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Hi Naama, I am trying to load the FF ontology used to describe samples from the FANTOM5 project: http://fantom.gsc.riken.jp/5/datafiles/latest/extra/Ontology/ff-phase2-140729.obo.txt Thank you so much for all the help, Mara On Mon, Apr 17, 2017 at 7:15 PM Naama Menda <naa...@gm...> wrote: > 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 >>>> >>>> |