[Gmod-help] Re: [Gmod-schema] Apollo and Chado problems
J.M.P. Alves
jmalves at vcu.edu
Wed Dec 2 16:11:29 EST 2009
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
>>
>>
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>
>
>
--
-------------------------------
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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