From: Eric R. <es...@ta...> - 2016-10-26 16:34:40
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Shane, Some notes about the prebuilt-schemas that my organisation hosts: - Our latest releases are available here: https://github.com/erasche/chado-schema-builder/releases. Hosting on github should be much more reliable than the copies hosted on my organisation's server. - We've recently produced images for 1.31, for a long while they had been out of date. Now they're being (semi-regularly) built again with fresh data! - As mentioned by Scott, we've switched the RO <https://github.com/erasche/chado-schema-builder/blob/master/load.conf.tt2#L45> out for one that works. Scott: no time like the present to try out the chado docker images <https://hub.docker.com/r/erasche/chado/> ;) Cheers, Eric ons. 26. okt. 2016 kl. 15.35 skrev Scott Cain <sc...@sc...>: > Hi Shane, > > The loader module, lib/Bio/GMOD/DB/Adaptor.pm, is quite old and uses an > ugly idiom that I'd rather not talk about but it's use has be deprecated in > modern Perl. I don't have a working instance of Chado I can test with > handy (later in the week I could spin something up on AWS, but I don't have > time now), but I did commit this to github if you want to try it out: > > > https://raw.githubusercontent.com/GMOD/Chado/fix_shift_if_defined/chado/lib/Bio/GMOD/DB/Adapter.pm > <https://urldefense.proofpoint.com/v2/url?u=https-3A__raw.githubusercontent.com_GMOD_Chado_fix-5Fshift-5Fif-5Fdefined_chado_lib_Bio_GMOD_DB_Adapter.pm&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=oxMjvL9zq_3ASiqEL_47oV1-hAH3Ss_sO9cZ4OQmCfo&e=> > > Just download this and replace the one it's complaining about in > /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm. > > Also, you won't be able to load the Relations Ontology via the make > command. You'll need to download > > http://purl.obolibrary.org/obo/ro/subsets/ro-chado.obo > <https://urldefense.proofpoint.com/v2/url?u=http-3A__purl.obolibrary.org_obo_ro_subsets_ro-2Dchado.obo&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=TzkzSeAw9RlbSkMGGODRqZc8HXazHWoEDWoZQ1ngUQk&e=> > > and use the commands described in INSTALL.Chado. In brief: > > $ go2fmt.pl > <https://urldefense.proofpoint.com/v2/url?u=http-3A__go2fmt.pl&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=sdfjunH0ATTldVhxMBtSE8a1UBO55HrvQRNrWyZA1xg&e=> > -p obo_text -w xml /path/to/obofile | \ > go-apply-xslt oboxml_to_chadoxml - > obo_text.xml > > and > > $ stag-storenode.pl > <https://urldefense.proofpoint.com/v2/url?u=http-3A__stag-2Dstorenode.pl&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=-FVBNPnYiIQ29Ag3WAn-PAX26CkRsx07zEOPARZpWp8&e=> > \ > -d 'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT' \ > --user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD obo_text.xml > > Depending on how you installed DBIx::DBStag, the ".pl" on > stag-storenode.pl > <https://urldefense.proofpoint.com/v2/url?u=http-3A__stag-2Dstorenode.pl&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=-FVBNPnYiIQ29Ag3WAn-PAX26CkRsx07zEOPARZpWp8&e=> > might have to be removed. > > Good luck! > Scott > > > On Wed, Oct 26, 2016 at 8:57 AM, Shane McCoy <sha...@gm...> > wrote: > > > > > > Hello, > > Using Chado VERSION=1.31 > > I am getting this error when using the gmod bulk load for Chado: > > > >> $ gmod_bulk_load_gff3.pl > <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod-5Fbulk-5Fload-5Fgff3.pl&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=99cqirF-J4zQD0Lz3ByPjnpyvymIyfBMo4SrKTg3THk&e=> > --noexon --analysis --organism "stripedbass" --gfffile > SBDraft_Full.nodna.gff --dbname apollo-db > >> Can't use 'defined(@array)' (Maybe you should just omit the defined()?) > at /usr/local/share/perl/5.22.1/Bio/GMOD/DB/Adapter.pm line 498. > >> Compilation failed in require at /usr/local/bin/gmod_bulk_load_gff3.pl > <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod-5Fbulk-5Fload-5Fgff3.pl&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=99cqirF-J4zQD0Lz3ByPjnpyvymIyfBMo4SrKTg3THk&e=> > line 13. > >> BEGIN failed--compilation aborted at /usr/local/bin/ > gmod_bulk_load_gff3.pl > <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod-5Fbulk-5Fload-5Fgff3.pl&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=99cqirF-J4zQD0Lz3ByPjnpyvymIyfBMo4SrKTg3THk&e=> > line 13. > > > > > > I have bioperl 1.006925 installed. I did see that the make ontologies > fails now, > >> > >> Which ontologies would you like to load (Comma delimited)? [0] 1,2,3,4 > >> fetching files for Relationship Ontology > >> +http://www.obofoundry.org/ro/ro.obo > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.obofoundry.org_ro_ro.obo&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=Eb2r0GJoa2JSwxPHl073N7jB8cutmXoEWS6STpqV3jw&e=> > >> 404 Not Found (http://www.obofoundry.org/ro/ro.obo > <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.obofoundry.org_ro_ro.obo&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=Eb2r0GJoa2JSwxPHl073N7jB8cutmXoEWS6STpqV3jw&e=> > ) > >> fetching files for Sequence Ontology > > > > > > I am using the > https://cpt.tamu.edu/computer-resources/chado-prebuilt-schema/ > recommended sql for this build. > > > > Any thoughts why this is failing? Thanks! > > Shane M. > > > > > > > > > > > ------------------------------------------------------------------------------ > > The Command Line: Reinvented for Modern Developers > > Did the resurgence of CLI tooling catch you by surprise? > > Reconnect with the command line and become more productive. > > Learn the new .NET and ASP.NET > <https://urldefense.proofpoint.com/v2/url?u=http-3A__ASP.NET&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=nKwFb83LeNaF3wApKFbnlxwN-UFyGstL2UtCUFnL-EI&e=> > CLI. Get your free copy! > > http://sdm.link/telerik > <https://urldefense.proofpoint.com/v2/url?u=http-3A__sdm.link_telerik&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=NlGNlOR4YjtjjADCZ_Qh6rCVLfJrnHm6auWtH0w62PQ&e=> > > _______________________________________________ > > Gmod-schema mailing list > > Gmo...@li... > > https://lists.sourceforge.net/lists/listinfo/gmod-schema > <https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.sourceforge.net_lists_listinfo_gmod-2Dschema&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=4oI_IKQKzs2lqp-Nv6o91SMm3HqytU4EpSio4QaSO18&e=> > > > > > > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. scott at scottcain > dot net > GMOD Coordinator (http://gmod.org/ > <https://urldefense.proofpoint.com/v2/url?u=http-3A__gmod.org_&d=CwMFaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=p9uZby14OqW9zcjBSjiDKw&m=gtn6y-LW0db_60v6RFs7tHr8LouDZZUkVl-wOnBdvJU&s=lNLOua1_XytvtZSfKsyGEBQrIZ3QpaUqUoAumzpbasw&e=>) > 216-392-3087 <(216)%20392-3087> > Ontario Institute for Cancer Research > > ------------------------------------------------------------------------------ > The Command Line: Reinvented for Modern Developers > Did the resurgence of CLI tooling catch you by surprise? > Reconnect with the command line and become more productive. > Learn the new .NET and ASP.NET CLI. Get your free copy! > http://sdm.link/telerik_______________________________________________ > Gmod-schema mailing list > Gmo...@li... > https://lists.sourceforge.net/lists/listinfo/gmod-schema > |