[Gmod-help] Re: [Gmod-schema] Apollo and Chado problems

Scott Cain scott at scottcain.net
Thu Dec 3 12:22:46 EST 2009 

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
>
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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