[Gmod-help] Re: [Gmod-schema] Apollo and Chado problems
J.M.P. Alves
jmalves at vcu.edu
Thu Dec 3 17:46:02 EST 2009
Hi,
At the end of loading the GFF file (using gmod_bulk_load_gff3.pl) into
Chado, I get something I did not get before:
commit ineffective with AutoCommit enabled
Is that just a warning and the data was loaded anyway, or does it mean
the commit failed? If I knew the schema better, I could check some
tables, but there are so many...
Thanks
J
Scott Cain wrote:
> Hi J,
>
> Yes, getting schema/trunk is sufficient. Since we moved to svn pretty
> recently, there are likely to be other holes in documentation where
> cvs was assumed.
>
> As for further questions, it depends on what they are concerning. If
> apollo webstart is causing you problems, you can ask about it on the
> apollo mailing list, GBrowse questions to the gbrowse list, and most
> other questions would go to the schema mailing list.
>
> Scott
>
> On Thu, Dec 3, 2009 at 12:15 PM, J.M.P. Alves <jmalves at vcu.edu> wrote:
>> Hi,
>>
>> Thanks for the answer, that helped. I was following the instructions from
>> http://gmod.org/wiki/Chado_-_Getting_Started but I missed the part about ant
>> (because I was originally not installing from SVN) -- have that installed
>> now. I didn't see anything about the checking out of the whole schema
>> though.
>>
>> What I did was this:
>>
>> svn co https://gmod.svn.sourceforge.net/svnroot/gmod/schema/trunk
>>
>> It does check out GMODTools and other stuff. Is that sufficient? It did take
>> care of all the errors at any rate.
>>
>> I'm now loading the ontologies into my database, and will next load the S.
>> cerevisiae GFF into the DB for testing (as described at
>> http://gmod.org/wiki/Load_GFF_Into_Chado).
>>
>> Thanks again
>> J
>>
>> PS: quick question, I'm using the community annotation server (VMware image
>> available from http://gmod.org/wiki/Community_Annotation_System) you have,
>> and it's mostly working (webstarted Apollo is giving a little trouble). I do
>> have some problems and questions about it though. Which list should I direct
>> them to?
>>
>>
>> Scott Cain wrote:
>>> Hi J,
>>>
>>> I don't know how I missed a few emails in this thread, but the problem
>>> you are having is because you need to checkout the entire schema
>>> repository, not just the chado subdirectory. You must have ant
>>> installed, and you need to have the GMODTools directory, which is at
>>> the same level as the chado directory.
>>>
>>> Scott
>>>
>>>
>>> On Wed, Dec 2, 2009 at 4:11 PM, J.M.P. Alves <jmalves at vcu.edu> wrote:
>>>> Hi, Dave
>>>>
>>>> Thanks, that did help -- although the two lines you mention were
>>>> *already*
>>>> commented out. I also had to comment out the following:
>>>>
>>>> if ($ant or !-e "$working_dir/../GMODTools") {
>>>> push @exe_files, 'bin/gmod_bulkfiles.pl', 'bin/gmod_gff2biomart5.pl';
>>>> }
>>>>
>>>> These are currently lines 493-5 of Makefile.PL
>>>>
>>>> After that, it did finish without problems, apparently.
>>>>
>>>> I am currently updating from the gmod-1.0 file found on SourceForge to
>>>> the
>>>> SVN code. Do I need to uninstall the old version (how? 'make uninstall'
>>>> does
>>>> not do it, just gives a list of things to delete) or is just installing
>>>> on
>>>> top of the one I have right now fine?
>>>>
>>>> Thanks
>>>> J
>>>>
>>>> Dave Clements, GMOD Help Desk wrote:
>>>>> Hi J,
>>>>>
>>>>> We generally recommend searching using Nabble:
>>>>> http://www.nabble.com/Generic-Model-Organism-System-Database-f3491.html
>>>>>
>>>>> And, using Nabble, I found a thread from 2007
>>>>>
>>>>> (http://old.nabble.com/Blast-input-file-for-CHADO-to9828403.html#a9847174)
>>>>> where someone had the same problem. I have no idea why you are having
>>>>> the problem, but a workaround is:
>>>>>
>>>>> But, it works after commenting out the following lines in Makefile.PL.
>>>>> #'bin/gmod_bulkfiles.pl', line no 522
>>>>> #'bin/gmod_gff2biomart5.pl', line no 523
>>>>>
>>>>> You don't need the biomart script unless you are using BioMart too.
>>>>> Does that work for you?
>>>>>
>>>>> Dave C.
>>>>>
>>>>> On Mon, Nov 30, 2009 at 1:44 PM, J.M.P. Alves <jmalves at vcu.edu> wrote:
>>>>>> Thanks, Scott
>>>>>>
>>>>>> I just subscribed to the list. BTW, is there a way to search it? I
>>>>>> looked there, but the Sourceforge interface is terrible, and the search
>>>>>> box on the top right searches all the site's project names instead of
>>>>>> the list archives.
>>>>>>
>>>>>> I ask because, following your advice, I checked out the svn version.
>>>>>> Then I got a warning during perl Makefile.PL that the kit was missing
>>>>>> files, contact author:
>>>>>>
>>>>>> ===========================================
>>>>>> Checking if your kit is complete...
>>>>>> Warning: the following files are missing in your kit:
>>>>>> bin/cxgn/load_cvterms.pl
>>>>>> bin/gmod_bulkfiles.pl
>>>>>> bin/gmod_gff2biomart5.pl
>>>>>> conf/bulkfiles/anogam.xml
>>>>>> conf/bulkfiles/blastfiles.xml
>>>>>> conf/bulkfiles/bulkfiles_template.xml
>>>>>> conf/bulkfiles/chadofeatconv.xml
>>>>>> conf/bulkfiles/chadofeatsql.xml
>>>>>> conf/bulkfiles/chadogenepagesql.xml
>>>>>> conf/bulkfiles/dmelhetfeatconv.xml
>>>>>> conf/bulkfiles/dmelr420.xml
>>>>>> conf/bulkfiles/dmelr430.xml
>>>>>> conf/bulkfiles/dpsebulk-p4.xml
>>>>>> conf/bulkfiles/dpsebulk-p5.xml
>>>>>> conf/bulkfiles/dpsebulk-r2.xml
>>>>>> conf/bulkfiles/drosmelgb.xml
>>>>>> conf/bulkfiles/fastawriter.xml
>>>>>> conf/bulkfiles/fbbulk-hetr3.xml
>>>>>> conf/bulkfiles/fbbulk-r3.xml
>>>>>> conf/bulkfiles/fbbulk-r3h.xml
>>>>>> conf/bulkfiles/fbbulk-r4.xml
>>>>>> conf/bulkfiles/fbbulk-r41.xml
>>>>>> conf/bulkfiles/fbbulk-r411.xml
>>>>>> conf/bulkfiles/fbreleases.xml
>>>>>> conf/bulkfiles/featuresets.xml
>>>>>> conf/bulkfiles/filesets.xml
>>>>>> conf/bulkfiles/gbrowseconf.xml
>>>>>> conf/bulkfiles/gbrowseconf_fb.xml
>>>>>> conf/bulkfiles/genbanksubmit.xml
>>>>>> conf/bulkfiles/genomeweb.xml
>>>>>> conf/bulkfiles/organisms.xml
>>>>>> conf/bulkfiles/sgdbulk.xml
>>>>>> conf/bulkfiles/sgdbulk1.xml
>>>>>> conf/bulkfiles/sgdfeatconf.xml
>>>>>> conf/bulkfiles/site_defaults.xml
>>>>>> conf/bulkfiles/site_eugenes_defaults.xml
>>>>>> conf/bulkfiles/spbase.xml
>>>>>> conf/bulkfiles/spbasefeatconf.xml
>>>>>> conf/bulkfiles/tablewriter.xml
>>>>>> conf/bulkfiles/toacode.xml
>>>>>> conf/bulkfiles/tognomap.xml
>>>>>> conf/chado2apollo-apache.conf
>>>>>> doc/about-gff2biomart.pod
>>>>>> doc/COPYRIGHT
>>>>>> doc/gff2biomart-update.note
>>>>>> doc/gmod-tools-readme.pod
>>>>>> lib/Bio/GMOD/Bulkfiles.pm
>>>>>> lib/Bio/GMOD/Bulkfiles/AcodeWriter.pm
>>>>>> lib/Bio/GMOD/Bulkfiles/BlastWriter.pm
>>>>>> lib/Bio/GMOD/Bulkfiles/BulkWriter.pm
>>>>>> lib/Bio/GMOD/Bulkfiles/FastaWriter.pm
>>>>>> lib/Bio/GMOD/Bulkfiles/FeatureWriter.pm
>>>>>> lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm
>>>>>> lib/Bio/GMOD/Bulkfiles/GnomapWriter.pm
>>>>>> lib/Bio/GMOD/Bulkfiles/MyLargePrimarySeq.pm
>>>>>> lib/Bio/GMOD/Bulkfiles/MySplitLocation.pm
>>>>>> lib/Bio/GMOD/Bulkfiles/SWISS_CRC64.pm
>>>>>> lib/Bio/GMOD/Bulkfiles/TableWriter.pm
>>>>>> lib/Bio/GMOD/Config2.pm
>>>>>> lib/Bio/GMOD/SeqUtils.pm
>>>>>> Please inform the author.
>>>>>> ===========================================
>>>>>>
>>>>>> When I "make", it finishes quite early, with:
>>>>>>
>>>>>> make: *** No rule to make target `bin/gmod_gff2biomart5.pl', needed by
>>>>>> `blib/script/gmod_gff2biomart5.pl'. Stop.
>>>>>>
>>>>>> (the full output of "make" is below)
>>>>>>
>>>>>> Has anyone seen this problem? Is it a problem? (it seems to me...) And
>>>>>> any idea what to do, please?
>>>>>>
>>>>>> Thanks
>>>>>> J
>>>>>>
>>>>>> ===========================================
>>>>>> ~/prog/chado$ make
>>>>>> Skip blib/lib/Bio/GMOD/Load.pm (unchanged)
>>>>>> Skip blib/lib/Bio/FeatureIO/chado.pm (unchanged)
>>>>>> Skip blib/lib/Bio/GMOD/DB/Config.pm (unchanged)
>>>>>> Skip blib/lib/Bio/Chado/Config.pm (unchanged)
>>>>>> Skip blib/lib/Bio/Chado/LoadDBI.pm (unchanged)
>>>>>> Skip blib/lib/Bio/GMOD/Load/GFF.pm (unchanged)
>>>>>> Skip blib/lib/Bio/GMOD/Config.pm (unchanged)
>>>>>> Skip blib/lib/Bio/FeatureIO/chadobulk.pm (unchanged)
>>>>>> Skip blib/lib/Bio/GMOD/DB/Adapter.pm (unchanged)
>>>>>> Skip blib/lib/Bio/GMOD/DB/Adapter/Wormbase.pm (unchanged)
>>>>>> Skip blib/lib/Bio/Chado/AutoDBI.pm (unchanged)
>>>>>> Skip blib/lib/Bio/GMOD/DB/Adapter/FeatureIterator.pm (unchanged)
>>>>>> Skip blib/lib/Bio/GMOD/DB/Tools/ETA.pm (unchanged)
>>>>>> Skip blib/lib/Bio/Chado/Builder.pm (unchanged)
>>>>>> make[1]: Entering directory `/home/jmalves/prog/chado/chaos-xml'
>>>>>> cp lib/Bio/Chaos/ChaosGraph.pm ../blib/lib/Bio/Chaos/ChaosGraph.pm
>>>>>> cp lib/Bio/Chaos/FeatureUtil.pm ../blib/lib/Bio/Chaos/FeatureUtil.pm
>>>>>> cp lib/Bio/Chaos/XSLTHelper.pm ../blib/lib/Bio/Chaos/XSLTHelper.pm
>>>>>> cp lib/Bio/Chaos/Root.pm ../blib/lib/Bio/Chaos/Root.pm
>>>>>> cp bin/cx-download-enscore.pl ../blib/script/cx-download-enscore.pl
>>>>>> /usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' --
>>>>>> ../blib/script/cx-download-enscore.pl
>>>>>> cp bin/cx-genbank2chaos.pl ../blib/script/cx-genbank2chaos.pl
>>>>>> /usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' --
>>>>>> ../blib/script/cx-genbank2chaos.pl
>>>>>> cp bin/cx-enscore2chaos.pl ../blib/script/cx-enscore2chaos.pl
>>>>>> /usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' --
>>>>>> ../blib/script/cx-enscore2chaos.pl
>>>>>> cp bin/cx-chadoxml2chaos.pl ../blib/script/cx-chadoxml2chaos.pl
>>>>>> /usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' --
>>>>>> ../blib/script/cx-chadoxml2chaos.pl
>>>>>> cp bin/cx-chaos-report.pl ../blib/script/cx-chaos-report.pl
>>>>>> /usr/bin/perl -MExtUtils::MY -e 'MY->fixin(shift)' --
>>>>>> ../blib/script/cx-chaos-report.pl
>>>>>> Manifying ../blib/man1/cx-genbank2chaos.pl.1p
>>>>>> Manifying ../blib/man1/cx-chadoxml2chaos.pl.1p
>>>>>> Manifying ../blib/man1/cx-chaos-report.pl.1p
>>>>>> Manifying ../blib/man3/Bio::Chaos::ChaosGraph.3pm
>>>>>> Manifying ../blib/man3/Bio::Chaos::FeatureUtil.3pm
>>>>>> Manifying ../blib/man3/Bio::Chaos::XSLTHelper.3pm
>>>>>> Manifying ../blib/man3/Bio::Chaos::Root.3pm
>>>>>> make[1]: Leaving directory `/home/jmalves/prog/chado/chaos-xml'
>>>>>> make: *** No rule to make target `bin/gmod_gff2biomart5.pl', needed by
>>>>>> `blib/script/gmod_gff2biomart5.pl'. Stop.
>>>>>> ===========================================
>>>>>>
>>>>>> Scott Cain wrote:
>>>>>>> Hello J,
>>>>>>>
>>>>>>> I'm cc'ing this response to the schema mailing list, which is where
>>>>>>> Chado discussion usually occurs. For the problem you are describing,
>>>>>>> there or the Apollo list (or both) would be a good place to start when
>>>>>>> looking for solutions.
>>>>>>>
>>>>>>> For using Apollo with Chado, I would suggest that you first take a
>>>>>>> look at the the tutorial on the GMOD website:
>>>>>>>
>>>>>>> http://gmod.org/wiki/Apollo_Tutorial
>>>>>>>
>>>>>>> Additionally, I would suggest you consider using chado checked out
>>>>>>> from svn instead of the 1.0 release; it is getting pretty old at this
>>>>>>> point. I am working on a 1.1 release that I plan to have out by the
>>>>>>> end of the year, but what is in svn now is quite stable.
>>>>>>>
>>>>>>> Scott
>>>>>>>
>>>>>>>
>>>>>>> On Wed, Nov 25, 2009 at 1:23 PM, J.M.P. Alves <jmalves at vcu.edu> wrote:
>>>>>>>> Hi,
>>>>>>>>
>>>>>>>> I am following the instructions from README.Apollo in the GMOD 1.0
>>>>>>>> distribution, and have found a couple of problems.
>>>>>>>>
>>>>>>>> When running
>>>>>>>>
>>>>>>>> psql chadodb < modules/sequence/apollo-bridge/apollo.inserts
>>>>>>>>
>>>>>>>> I got a couple of errors. The first:
>>>>>>>>
>>>>>>>> ERROR: null value in column "cv_id" violates not-null constraint
>>>>>>>>
>>>>>>>> I checked the offending part of the sql and it tries to find a cv_if
>>>>>>>> for the
>>>>>>>> record with "Relationship Ontology" as name. But in the schema I
>>>>>>>> installed
>>>>>>>> there is no such record. The closest I could find was one called
>>>>>>>> "relationship" and one called "pub relationship type". Which is the
>>>>>>>> correct
>>>>>>>> one?
>>>>>>>>
>>>>>>>> The second error was:
>>>>>>>>
>>>>>>>> ERROR: aggregates not allowed in WHERE clause
>>>>>>>>
>>>>>>>> This was triggered by the command:
>>>>>>>>
>>>>>>>> delete from feature_namegenerator where feature_namegenerator_id not
>>>>>>>> in
>>>>>>>> (select feature_namegenerator_id from feature_namegenerator where
>>>>>>>> count
>>>>>>>> =
>>>>>>>> max(count) group by name,type_id);
>>>>>>>>
>>>>>>>> I haven't figured out how to solve this one, since I have no
>>>>>>>> experience
>>>>>>>> with
>>>>>>>> PostgreSQL.
>>>>>>>>
>>>>>>>> Regards
>>>>>>>> J
>>>>>>>>
>>>>>>>>
>>>>>>>> P.S.: I wrote a few minutes ago about a problem with GBrowse's Chado
>>>>>>>> documentation. I spoke too soon, there was another problem that I
>>>>>>>> found
>>>>>>>> when
>>>>>>>> I clicked on the examples in GBrowse (gene name). Adding the
>>>>>>>> following
>>>>>>>> table
>>>>>>>> to the permissions solved it:
>>>>>>>>
>>>>>>>> GRANT SELECT ON all_feature_names TO "www-data";
>>>>>>>>
>>>>>>>> --
>>>>>>>> -------------------------------
>>>>>>>> João Marcelo Pereira Alves (J)
>>>>>>>> Post-doctoral fellow
>>>>>>>> MCV / VCU - Richmond, VA
>>>>>>>> http://bioinfo.lpb.mic.vcu.edu
>>>>>>>> f. 1-804-828-3897
>>>>>>>>
>>>>>>>>
>>>>>> --
>>>>>> -------------------------------
>>>>>> João Marcelo Pereira Alves (J)
>>>>>> Post-doctoral fellow
>>>>>> MCV / VCU - Richmond, VA
>>>>>> http://bioinfo.lpb.mic.vcu.edu
>>>>>> f. 1-804-828-3897
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>> Join us December 9, 2009 for the Red Hat Virtual Experience,
>>>>>> a free event focused on virtualization and cloud computing.
>>>>>> Attend in-depth sessions from your desk. Your couch. Anywhere.
>>>>>> http://p.sf.net/sfu/redhat-sfdev2dev
>>>>>> _______________________________________________
>>>>>> Gmod-schema mailing list
>>>>>> Gmod-schema at lists.sourceforge.net
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>
>>>>>
>>>> --
>>>> -------------------------------
>>>> João Marcelo Pereira Alves (J)
>>>> Post-doctoral fellow
>>>> MCV / VCU - Richmond, VA
>>>> http://bioinfo.lpb.mic.vcu.edu
>>>> f. 1-804-828-3897
>>>>
>>>>
>>>>
>>>
>>>
>> --
>> -------------------------------
>> João Marcelo Pereira Alves (J)
>> Post-doctoral fellow
>> MCV / VCU - Richmond, VA
>> http://bioinfo.lpb.mic.vcu.edu
>> f. 1-804-828-3897
>>
>>
>
>
>
--
-------------------------------
João Marcelo Pereira Alves (J)
Post-doctoral fellow
MCV / VCU - Richmond, VA
http://bioinfo.lpb.mic.vcu.edu
f. 1-804-828-3897
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