From: Shane M. <sha...@gm...> - 2016-10-26 21:26:32
|
Thanks Eric! I wasn't aware of this resource. I downloaded chado-1.31.sql.gz and used the Apollo script to upload to db. Easiest setup yet! thanks! > /Apollo$ *scripts/load_chado_schema.sh -u bjreadin -d apollo-db -h > localhost -p 5432 -r -s scripts/chado-1.31.sql.gz* > ERROR: database "apollo-db" already exists > Database 'apollo-db' already exists. Backing up data via pg_dump. > pg_dump -U bjreadin -d apollo-db -h localhost -p 5432 -f > apollo-db_database_dump_2016-10-26_16:11:20.sql -b > pg_dump was successful. > Dropping and creating database 'apollo-db'. > DROP DATABASE > CREATE DATABASE > Loading chado schema scripts/chado-1.31.sql.gz to database 'apollo-db'. > Chado schema loaded successfully to apollo-db. Check > load_chado_schema_2016-10-26_16:11:20.log for more information. On Wed, Oct 26, 2016 at 12:08 PM, Eric Rasche <es...@ta...> wrote: > 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 been out of date.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 >> > |