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From: Poliana M. <pol...@gm...> - 2005-02-21 17:22:39
|
In your directory /usr/local/src/gus-related/ontology/ exist the file "component.ontology"?? Poliana On Mon, 21 Feb 2005 18:18:53 +0100 (CET), fed...@bi... <fed...@bi...> wrote: > Thanks Poliana! > For LoadTaxon it's ok!!! > For GoOntology I always have the same error: >=20 > ga GUS::GOPredict::Plugin::LoadGoOntology \ > > --file_path=3D/usr/local/src/gus-related/ontology/ \ > > --process_db_id=3D3003 \ > > --process_ext_db_rel=3D6 \ > > --function_db_id=3D3001 \ > > --function_ext_db_rel=3D33 \ > > --component_db_id=3D3002 \ > > --component_ext_db_rel=3D28 \ > > --create_release > /usr/local/src/gus-related/ontology/Mon Feb 21 18:02:13 2005 loading > all .ontology files in /usr/local/src/gus-related/ontology/ in preparatio= n > for parsing > Note: did not find file component.ontology in directory > CBIL::Bio::GeneOntologyParser::Parser=3DHASH(0x89d2380)->getPath. > To load this branch of the ontology specified by component.ontology, > please put that file in the directory. > Note: did not find file process.ontology in directory > CBIL::Bio::GeneOntologyParser::Parser=3DHASH(0x89d2380)->getPath. > To load this branch of the ontology specified by process.ontology, > please put that file in the directory. > Note: did not find file function.ontology in directory > CBIL::Bio::GeneOntologyParser::Parser=3DHASH(0x89d2380)->getPath. > To load this branch of the ontology specified by function.ontology, > please put that file in the directory. > Mon Feb 21 18:02:13 2005 parsing all .ontology files in preparatio= n > for inserting into database > Mon Feb 21 18:02:13 2005 parsing finished; loading ontology into > database > Mon Feb 21 18:02:13 2005 RESULT Created 0 entries in GOTerm, 0 > entries in GORelationship, and 0 entries in GOSynonym. Skipped 0 total > entries >=20 > I understand it's a problem releted with che *.ontology path, but I reall= y > don't know where I have to put my files! I think it suggests the path > ..../CBIL/Bio/GeneOntologyParser: I put there my files but nothing > changed! > Do you understand something more? > Cheers > Federica >=20 >=20 > > Hi Federica, > > > > I run thus: > > > > GoOntology: > > > > ga GUS::GOPredict::Plugin::LoadGoOntology > > --file_path=3D/usr/local/db/local/ontology/ --process_db_id=3D3003 > > --process_ext_db_rel=3D6 --function_db_id=3D3001 --function_ext_db_rel= =3D33 > > --component_db_id=3D3002 =C3=A2=E2=82=AC"component_ext_db_rel=3D28 --c= reate_release > > > > See if your files (*.ontology) are in the correct path. > > > > ***********************************************************************= **************************** > > > > LoadTaxon: > > > > ga GUS::Common::Plugin::LoadTaxon > > -gencode=3D/usr/local/db/local/taxonomy/gencode.dmp > > --names=3D/usr/local/db/local/taxonomy/names.dmp > > --nodes=3D/usr/local/db/local/taxonomy/nodes.dmp > > --merged=3D/usr/local/db/local/taxonomy/merged.dmp > > > > > > Change for its your path.... > > > > Poliana > > > > > > On Mon, 21 Feb 2005 16:37:22 +0100 (CET), fed...@bi... > > <fed...@bi...> wrote: > >> Thanks, but I've downloaded from there, and I also have right > >> privileges...! > >> I tried also to include merged.dmp even if it's not named in the > >> bootstrap > >> instructions!! But nothing good happened! > >> Any other suggestions? > >> Federica > >> > >> > >> > For LoadTaxon, you need to supply the names with path for all for > >> file, > >> > gencode.dmp,name.dmp,nodes.dump,merged.dmp. These files are download= ed > >> > from NCBI (ftp://ftp.ncbi.nih.gov/pub/taxonomy) as a tarball, > >> > taxdump.tar.Z or taxdump.tar.gz and uncompressed. > >> > > >> > > >> > Debbie > >> > > >> > > >> > > >> > > >> > > >> > > >> > fed...@bi... wrote: > >> > > >> >>Hi everybody! > >> >>I'm here again! I'm inserting data following the bootstrap but I had > >> this > >> >>errors: > >> >>1) for Taxonomy > >> >>$ ga GUS::Common::Plugin::LoadTaxon \ > >> >> > >> >> > >> >>>--gencode=3D/usr/local/src/gus_related/taxonomy/gencode.dmp \ > >> >>>--names=3D/usr/local/src/gus_related/taxonomy/names.dmp \ > >> >>>--nodes=3D/usr/local/src/gus_related/taxonomy/nodes.dmp > >> >>> > >> >>> > >> >>ERROR: The names of the names.dmp, nodes.dmp, gencode.dmp and > >> merged.dmp > >> >>files must > >> >>be provided on the command line. > >> >>2) for GO Ontology > >> >>$ ga GUS::GOPredict::Plugin::LoadGoOntology > >> >>--file_path=3D/usr/local/src/gus-related/ontology/ \ > >> >> > >> >> > >> >>>--process_db_id=3D3003 \ > >> >>>--process_ext_db_rel=3D165 \ > >> >>>--function_db_id=3D3001 \ > >> >>>--function_ext_db_rel=3D164 \ > >> >>>--component_db_id=3D3002 \ > >> >>>--component_ext_db_rel=3D166 \ > >> >>> > >> >>> > >> >> > >> >>/usr/local/src/gus-related/ontology/Mon Feb 21 15:45:51 2005 > >> loading > >> >> all > >> >>.ontology files in /usr/local/src/gus-related/ontology/ in preparati= on > >> >> for > >> >>parsing > >> >>Note: did not find file component.ontology in directory > >> >>CBIL::Bio::GeneOntologyParser::Parser=3DHASH(0x89d2180)->getPath. > >> >> To load this branch of the ontology specified by component.ontology= , > >> >> please put that file in the directory. > >> >>Note: did not find file process.ontology in directory > >> >>CBIL::Bio::GeneOntologyParser::Parser=3DHASH(0x89d2180)->getPath. > >> >> To load this branch of the ontology specified by process.ontology, > >> >> please put that file in the directory. > >> >>Note: did not find file function.ontology in directory > >> >>CBIL::Bio::GeneOntologyParser::Parser=3DHASH(0x89d2180)->getPath. > >> >> To load this branch of the ontology specified by function.ontology, > >> >> please put that file in the directory. > >> >>Mon Feb 21 15:45:51 2005 parsing all .ontology files in > >> >> preparation > >> >>for > >> >>inserting into database > >> >>Mon Feb 21 15:45:51 2005 parsing finished; loading ontology > >> into > >> >>database > >> >>Mon Feb 21 15:45:51 2005 RESULT Created 0 entries in GOTerm,= 0 > >> >>entries in > >> >>GORelationship, and 0 entries in GOSynonym. Skipped 0 total entries > >> >> > >> >>Any help? > >> >>Cheers, > >> >>Federica > >> >> > >> >> > >> >> > >> >>------------------------------------------------------- > >> >>SF email is sponsored by - The IT Product Guide > >> >>Read honest & candid reviews on hundreds of IT Products from real > >> users. > >> >>Discover which products truly live up to the hype. Start reading now= . > >> >>http://ads.osdn.com/?ad_id=3D6595&alloc_id=3D14396&op=3Dclick > >> >>_______________________________________________ > >> >>Gusdev-gusdev mailing list > >> >>Gus...@li... > >> >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > >> >> > >> >> > >> > > >> > > >> > >> ------------------------------------------------------- > >> SF email is sponsored by - The IT Product Guide > >> Read honest & candid reviews on hundreds of IT Products from real user= s. > >> Discover which products truly live up to the hype. Start reading now. > >> http://ads.osdn.com/?ad_id=3D6595&alloc_id=3D14396&op=3Dclick > >> _______________________________________________ > >> Gusdev-gusdev mailing list > >> Gus...@li... > >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > >> > > >=20 > |
|
From: Poliana M. <pol...@gm...> - 2005-02-21 15:49:58
|
Hi Federica,
I run thus:
GoOntology:
ga GUS::GOPredict::Plugin::LoadGoOntology
--file_path=3D/usr/local/db/local/ontology/ --process_db_id=3D3003
--process_ext_db_rel=3D6 --function_db_id=3D3001 --function_ext_db_rel=3D33
--component_db_id=3D3002 =E2=80=93component_ext_db_rel=3D28 --create_relea=
se
See if your files (*.ontology) are in the correct path.
***************************************************************************=
************************
LoadTaxon:
ga GUS::Common::Plugin::LoadTaxon
-gencode=3D/usr/local/db/local/taxonomy/gencode.dmp
--names=3D/usr/local/db/local/taxonomy/names.dmp
--nodes=3D/usr/local/db/local/taxonomy/nodes.dmp
--merged=3D/usr/local/db/local/taxonomy/merged.dmp =20
Change for its your path....
Poliana
On Mon, 21 Feb 2005 16:37:22 +0100 (CET), fed...@bi...
<fed...@bi...> wrote:
> Thanks, but I've downloaded from there, and I also have right privileges.=
..!
> I tried also to include merged.dmp even if it's not named in the bootstra=
p
> instructions!! But nothing good happened!
> Any other suggestions?
> Federica
>=20
>=20
> > For LoadTaxon, you need to supply the names with path for all for file,
> > gencode.dmp,name.dmp,nodes.dump,merged.dmp. These files are downloaded
> > from NCBI (ftp://ftp.ncbi.nih.gov/pub/taxonomy) as a tarball,
> > taxdump.tar.Z or taxdump.tar.gz and uncompressed.
> >
> >
> > Debbie
> >
> >
> >
> >
> >
> >
> > fed...@bi... wrote:
> >
> >>Hi everybody!
> >>I'm here again! I'm inserting data following the bootstrap but I had th=
is
> >>errors:
> >>1) for Taxonomy
> >>$ ga GUS::Common::Plugin::LoadTaxon \
> >>
> >>
> >>>--gencode=3D/usr/local/src/gus_related/taxonomy/gencode.dmp \
> >>>--names=3D/usr/local/src/gus_related/taxonomy/names.dmp \
> >>>--nodes=3D/usr/local/src/gus_related/taxonomy/nodes.dmp
> >>>
> >>>
> >>ERROR: The names of the names.dmp, nodes.dmp, gencode.dmp and merged.dm=
p
> >>files must
> >>be provided on the command line.
> >>2) for GO Ontology
> >>$ ga GUS::GOPredict::Plugin::LoadGoOntology
> >>--file_path=3D/usr/local/src/gus-related/ontology/ \
> >>
> >>
> >>>--process_db_id=3D3003 \
> >>>--process_ext_db_rel=3D165 \
> >>>--function_db_id=3D3001 \
> >>>--function_ext_db_rel=3D164 \
> >>>--component_db_id=3D3002 \
> >>>--component_ext_db_rel=3D166 \
> >>>
> >>>
> >>
> >>/usr/local/src/gus-related/ontology/Mon Feb 21 15:45:51 2005 loading
> >> all
> >>.ontology files in /usr/local/src/gus-related/ontology/ in preparation
> >> for
> >>parsing
> >>Note: did not find file component.ontology in directory
> >>CBIL::Bio::GeneOntologyParser::Parser=3DHASH(0x89d2180)->getPath.
> >> To load this branch of the ontology specified by component.ontology,
> >> please put that file in the directory.
> >>Note: did not find file process.ontology in directory
> >>CBIL::Bio::GeneOntologyParser::Parser=3DHASH(0x89d2180)->getPath.
> >> To load this branch of the ontology specified by process.ontology,
> >> please put that file in the directory.
> >>Note: did not find file function.ontology in directory
> >>CBIL::Bio::GeneOntologyParser::Parser=3DHASH(0x89d2180)->getPath.
> >> To load this branch of the ontology specified by function.ontology,
> >> please put that file in the directory.
> >>Mon Feb 21 15:45:51 2005 parsing all .ontology files in
> >> preparation
> >>for
> >>inserting into database
> >>Mon Feb 21 15:45:51 2005 parsing finished; loading ontology into
> >>database
> >>Mon Feb 21 15:45:51 2005 RESULT Created 0 entries in GOTerm, 0
> >>entries in
> >>GORelationship, and 0 entries in GOSynonym. Skipped 0 total entries
> >>
> >>Any help?
> >>Cheers,
> >>Federica
> >>
> >>
> >>
> >>-------------------------------------------------------
> >>SF email is sponsored by - The IT Product Guide
> >>Read honest & candid reviews on hundreds of IT Products from real users=
.
> >>Discover which products truly live up to the hype. Start reading now.
> >>http://ads.osdn.com/?ad_id=3D6595&alloc_id=3D14396&op=3Dclick
> >>_______________________________________________
> >>Gusdev-gusdev mailing list
> >>Gus...@li...
> >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> >>
> >>
> >
> >
>=20
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
> http://ads.osdn.com/?ad_id=3D6595&alloc_id=3D14396&op=3Dclick
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: <fed...@bi...> - 2005-02-21 15:37:33
|
Thanks, but I've downloaded from there, and I also have right privileges...! I tried also to include merged.dmp even if it's not named in the bootstrap instructions!! But nothing good happened! Any other suggestions? Federica > For LoadTaxon, you need to supply the names with path for all for file, > gencode.dmp,name.dmp,nodes.dump,merged.dmp. These files are downloaded > from NCBI (ftp://ftp.ncbi.nih.gov/pub/taxonomy) as a tarball, > taxdump.tar.Z or taxdump.tar.gz and uncompressed. > > > Debbie > > > > > > > fed...@bi... wrote: > >>Hi everybody! >>I'm here again! I'm inserting data following the bootstrap but I had this >>errors: >>1) for Taxonomy >>$ ga GUS::Common::Plugin::LoadTaxon \ >> >> >>>--gencode=/usr/local/src/gus_related/taxonomy/gencode.dmp \ >>>--names=/usr/local/src/gus_related/taxonomy/names.dmp \ >>>--nodes=/usr/local/src/gus_related/taxonomy/nodes.dmp >>> >>> >>ERROR: The names of the names.dmp, nodes.dmp, gencode.dmp and merged.dmp >>files must >>be provided on the command line. >>2) for GO Ontology >>$ ga GUS::GOPredict::Plugin::LoadGoOntology >>--file_path=/usr/local/src/gus-related/ontology/ \ >> >> >>>--process_db_id=3003 \ >>>--process_ext_db_rel=165 \ >>>--function_db_id=3001 \ >>>--function_ext_db_rel=164 \ >>>--component_db_id=3002 \ >>>--component_ext_db_rel=166 \ >>> >>> >> >>/usr/local/src/gus-related/ontology/Mon Feb 21 15:45:51 2005 loading >> all >>.ontology files in /usr/local/src/gus-related/ontology/ in preparation >> for >>parsing >>Note: did not find file component.ontology in directory >>CBIL::Bio::GeneOntologyParser::Parser=HASH(0x89d2180)->getPath. >> To load this branch of the ontology specified by component.ontology, >> please put that file in the directory. >>Note: did not find file process.ontology in directory >>CBIL::Bio::GeneOntologyParser::Parser=HASH(0x89d2180)->getPath. >> To load this branch of the ontology specified by process.ontology, >> please put that file in the directory. >>Note: did not find file function.ontology in directory >>CBIL::Bio::GeneOntologyParser::Parser=HASH(0x89d2180)->getPath. >> To load this branch of the ontology specified by function.ontology, >> please put that file in the directory. >>Mon Feb 21 15:45:51 2005 parsing all .ontology files in >> preparation >>for >>inserting into database >>Mon Feb 21 15:45:51 2005 parsing finished; loading ontology into >>database >>Mon Feb 21 15:45:51 2005 RESULT Created 0 entries in GOTerm, 0 >>entries in >>GORelationship, and 0 entries in GOSynonym. Skipped 0 total entries >> >>Any help? >>Cheers, >>Federica >> >> >> >>------------------------------------------------------- >>SF email is sponsored by - The IT Product Guide >>Read honest & candid reviews on hundreds of IT Products from real users. >>Discover which products truly live up to the hype. Start reading now. >>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >>_______________________________________________ >>Gusdev-gusdev mailing list >>Gus...@li... >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> > > |
|
From: Deborah P. <pi...@pc...> - 2005-02-21 15:18:37
|
For LoadTaxon, you need to supply the names with path for all for file, gencode.dmp,name.dmp,nodes.dump,merged.dmp. These files are downloaded from NCBI (ftp://ftp.ncbi.nih.gov/pub/taxonomy) as a tarball, taxdump.tar.Z or taxdump.tar.gz and uncompressed. Debbie fed...@bi... wrote: >Hi everybody! >I'm here again! I'm inserting data following the bootstrap but I had this >errors: >1) for Taxonomy >$ ga GUS::Common::Plugin::LoadTaxon \ > > >>--gencode=/usr/local/src/gus_related/taxonomy/gencode.dmp \ >>--names=/usr/local/src/gus_related/taxonomy/names.dmp \ >>--nodes=/usr/local/src/gus_related/taxonomy/nodes.dmp >> >> >ERROR: The names of the names.dmp, nodes.dmp, gencode.dmp and merged.dmp >files must >be provided on the command line. >2) for GO Ontology >$ ga GUS::GOPredict::Plugin::LoadGoOntology >--file_path=/usr/local/src/gus-related/ontology/ \ > > >>--process_db_id=3003 \ >>--process_ext_db_rel=165 \ >>--function_db_id=3001 \ >>--function_ext_db_rel=164 \ >>--component_db_id=3002 \ >>--component_ext_db_rel=166 \ >> >> > >/usr/local/src/gus-related/ontology/Mon Feb 21 15:45:51 2005 loading all >.ontology files in /usr/local/src/gus-related/ontology/ in preparation for >parsing >Note: did not find file component.ontology in directory >CBIL::Bio::GeneOntologyParser::Parser=HASH(0x89d2180)->getPath. > To load this branch of the ontology specified by component.ontology, > please put that file in the directory. >Note: did not find file process.ontology in directory >CBIL::Bio::GeneOntologyParser::Parser=HASH(0x89d2180)->getPath. > To load this branch of the ontology specified by process.ontology, > please put that file in the directory. >Note: did not find file function.ontology in directory >CBIL::Bio::GeneOntologyParser::Parser=HASH(0x89d2180)->getPath. > To load this branch of the ontology specified by function.ontology, > please put that file in the directory. >Mon Feb 21 15:45:51 2005 parsing all .ontology files in preparation >for >inserting into database >Mon Feb 21 15:45:51 2005 parsing finished; loading ontology into >database >Mon Feb 21 15:45:51 2005 RESULT Created 0 entries in GOTerm, 0 >entries in >GORelationship, and 0 entries in GOSynonym. Skipped 0 total entries > >Any help? >Cheers, >Federica > > > >------------------------------------------------------- >SF email is sponsored by - The IT Product Guide >Read honest & candid reviews on hundreds of IT Products from real users. >Discover which products truly live up to the hype. Start reading now. >http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
|
From: <fed...@bi...> - 2005-02-21 15:01:52
|
Hi everybody! I'm here again! I'm inserting data following the bootstrap but I had this errors: 1) for Taxonomy $ ga GUS::Common::Plugin::LoadTaxon \ > --gencode=/usr/local/src/gus_related/taxonomy/gencode.dmp \ > --names=/usr/local/src/gus_related/taxonomy/names.dmp \ > --nodes=/usr/local/src/gus_related/taxonomy/nodes.dmp ERROR: The names of the names.dmp, nodes.dmp, gencode.dmp and merged.dmp files must be provided on the command line. 2) for GO Ontology $ ga GUS::GOPredict::Plugin::LoadGoOntology --file_path=/usr/local/src/gus-related/ontology/ \ > --process_db_id=3003 \ > --process_ext_db_rel=165 \ > --function_db_id=3001 \ > --function_ext_db_rel=164 \ > --component_db_id=3002 \ > --component_ext_db_rel=166 \ /usr/local/src/gus-related/ontology/Mon Feb 21 15:45:51 2005 loading all .ontology files in /usr/local/src/gus-related/ontology/ in preparation for parsing Note: did not find file component.ontology in directory CBIL::Bio::GeneOntologyParser::Parser=HASH(0x89d2180)->getPath. To load this branch of the ontology specified by component.ontology, please put that file in the directory. Note: did not find file process.ontology in directory CBIL::Bio::GeneOntologyParser::Parser=HASH(0x89d2180)->getPath. To load this branch of the ontology specified by process.ontology, please put that file in the directory. Note: did not find file function.ontology in directory CBIL::Bio::GeneOntologyParser::Parser=HASH(0x89d2180)->getPath. To load this branch of the ontology specified by function.ontology, please put that file in the directory. Mon Feb 21 15:45:51 2005 parsing all .ontology files in preparation for inserting into database Mon Feb 21 15:45:51 2005 parsing finished; loading ontology into database Mon Feb 21 15:45:51 2005 RESULT Created 0 entries in GOTerm, 0 entries in GORelationship, and 0 entries in GOSynonym. Skipped 0 total entries Any help? Cheers, Federica |
|
From: Deborah P. <pi...@pc...> - 2005-02-18 17:53:07
|
I believe it inserts into the version table by selecting the row in the
nasequenceimp table, therefore you have put the current row in the
version table. It needs to version before it inserts or updates. Make
sure the dates used are to the second, otherwise you will get a lot of
these. We have discussed changing the PK defintion for the version
tables because computers can run too fast to avoid this sort of problem
at times even if the time is taken to the second.
In short, you aren't really versioning anymore and when you rerun this
plugin or another to version the same row, you will get the problem you
tried to avoid. However, this will happen a lot more.
Debbie
Jeetendra Soneja wrote:
>Hi all
>
>I am trying to update a genbank sequence using GBParser plugin. While
>updating I got an error during versioning, for trying to insert a
>duplicate value for the primary key in dotsver.externalnasequencever (i.e.
>dotsver.nasequenceimpver) table.
>
>While debugging I figured out that the primary key for the
>dotsver.nasequenceimpver table is the combination of na_sequence_id and
>modification_date. However, the order of the statements in GusRow.pm
>module is
>
> $self->version();
> $self->update();
>
>Thus, it is trying to version before updating the sequence. That it, it is
>inserting a row with identical na_sequence_id and modification_date (using
>insert statement with 'select * from dots.externalnasequence') in the
>version table.
>
>When I swapped the order of these statements so that the update statement
>executes first, it worked fine.
>
>Also, one more concern is that the above combination for the primary key
>of the verion tables would allow updating a sequence only once for any
>date.
>
>Any suggestions/comments are welcome.
>
>Thanks,
>Jeetendra.
>
>
>
>-------------------------------------------------------
>SF email is sponsored by - The IT Product Guide
>Read honest & candid reviews on hundreds of IT Products from real users.
>Discover which products truly live up to the hype. Start reading now.
>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>_______________________________________________
>Gusdev-gusdev mailing list
>Gus...@li...
>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>
|
|
From: Jeetendra S. <so...@vb...> - 2005-02-18 17:12:08
|
Hi all I am trying to update a genbank sequence using GBParser plugin. While updating I got an error during versioning, for trying to insert a duplicate value for the primary key in dotsver.externalnasequencever (i.e. dotsver.nasequenceimpver) table. While debugging I figured out that the primary key for the dotsver.nasequenceimpver table is the combination of na_sequence_id and modification_date. However, the order of the statements in GusRow.pm module is $self->version(); $self->update(); Thus, it is trying to version before updating the sequence. That it, it is inserting a row with identical na_sequence_id and modification_date (using insert statement with 'select * from dots.externalnasequence') in the version table. When I swapped the order of these statements so that the update statement executes first, it worked fine. Also, one more concern is that the above combination for the primary key of the verion tables would allow updating a sequence only once for any date. Any suggestions/comments are welcome. Thanks, Jeetendra. |
|
From: Ed R. <ero...@ug...> - 2005-02-18 16:32:33
|
NAFeatureImp is a table you should NEVER write to. It is essentially an object master class. The GUS features you want to write to are all views. These include Dots.RNAType, Dots.GeneFeature, Dots.Transcript. GUS uses sub-classing to create the different kinds of features you load and store. These subclasses are accessed through the views. These views alias the different generic string/int/tiny fields in NAFeatureImp to give them real property names. All sub_class views of NA_Feature_Imp inheirit the named attributes of the IMP table. However, ONLY the views keep track of which generic fields are mapped to what properties. So, only use the views to access this table, otherwise, you may corrupt your data. The same goes for NASequenceImp, AAFeatureImp and AASequenceImp. -ed ---- Original message ---- >Date: Fri, 18 Feb 2005 14:13:29 -0200 >From: Alberto Davila <da...@io...> >Subject: Re: [Gusdev-gusdev] parseBlastFilesForSimilarity.pl >To: Steve Fischer <sfi...@pc...> >Cc: Josef Jurek <ju...@cs...>, gus...@li..., pol...@gm... > >Hi Steve, > >Yesterday Poliana presented an internal seminar about GUS (focused on >tables used by GBParser and GlimmerM), then some questions arised, maybe >you (or someone else) could help: > >Why we need several "string" columns in "DoTs.NASequenceImp": > >DoTs.NASequenceImp >string1 >string2 >string3 >string4 >string5 > >What should be stored in the columns of DoTs.FeatureImp : > >DoTs.FeatureImp >int1 ... int6 >tinyint1 ... tinyint6 >float1 ... float6 >text1 >string1 ... string50 > >Finally, (I think this is for Bindu) does the current version of the >"ImportPlasmoDBPrediction" plugin support more than one ORF predicted by >GlimmerM ? in other words, GlimmerM usually present several rows of >predicted ORFs, each one with a score probability, and there might be >more than one ORF predicted... and more than one can be a valid ORF... > >Thanks, Alberto > >On Thu, 2005-02-17 at 15:59 -0500, Steve Fischer wrote: >> luckily we are already adding that in 3.5 >> >> see AnalysisAlgorithm in the 3.5 roadmap: >> http://www.gusdb.org/wiki/index.php/Gus3.5RoadMap >> >> steve >> >> Josef Jurek wrote: >> >> >Concerning the DoTS.Similarity table which has been discussed >> >recently, what we at the Preuss lab are really hurting for >> >is a way to distinguish different Blast analyses (different >> >blast parameters) of the same subject and query sequences. >> >A table as simple as: >> > >> > id number(10) >> > name varchar2(255) >> > parameters varchar2(255) >> > >> >so that one could store something as simple as: >> > >> > 'Param Set 001' >> > '-p blastx -M BLOSUM50 -G 13 -E 2 -e .01 -W 3' >> > >> >and a way to link these entries to the rows of >> >DoTS.Similarity, perhaps in the way that >> >DoTS.NASequenceKeyword links rows of DoTS.NASequence >> >and DoTS.Keyword, would work. If we were to go ahead and >> >add the table to the schema, we might want to actually >> >list the parameters individually with a >> >comment string, perhaps like: >> > >> > >> > name varchar2(255) >> > ... >> > expectation_threshold float(22) >> > gap_penalty_existence number(10) >> > gap_penalty_extension number(10) >> > ... >> > comment varchar2(255) >> > >> >Are not other people on the list >> >missing the ability to distinguish >> >blast results by parameters? >> > >> >Thanks, Josef >> > >> > >> > >> >Josef Jurek, Ph.D. >> > >> >Daphne Preuss Laboratory >> >Molecular Genetics and Cell Biology >> >The University of Chicago >> >ju...@cs... >> > >> >voice: (773) 834-3985 >> >fax: (773) 702-6648 >> > >> > > > > >------------------------------------------------------- >SF email is sponsored by - The IT Product Guide >Read honest & candid reviews on hundreds of IT Products from real users. >Discover which products truly live up to the hype. Start reading now. >http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev ----------------- Ed Robinson Center for Tropical and Emerging Global Diseases University of Georgia, Athens, GA 30602 ero...@ug.../(706)542.1447/254.8883 |
|
From: Alberto D. <da...@io...> - 2005-02-18 16:04:41
|
Hi Steve, Yesterday Poliana presented an internal seminar about GUS (focused on tables used by GBParser and GlimmerM), then some questions arised, maybe you (or someone else) could help: Why we need several "string" columns in "DoTs.NASequenceImp": DoTs.NASequenceImp string1 string2 string3 string4 string5 What should be stored in the columns of DoTs.FeatureImp : DoTs.FeatureImp int1 ... int6 tinyint1 ... tinyint6 float1 ... float6 text1 string1 ... string50 Finally, (I think this is for Bindu) does the current version of the "ImportPlasmoDBPrediction" plugin support more than one ORF predicted by GlimmerM ? in other words, GlimmerM usually present several rows of predicted ORFs, each one with a score probability, and there might be more than one ORF predicted... and more than one can be a valid ORF... Thanks, Alberto On Thu, 2005-02-17 at 15:59 -0500, Steve Fischer wrote: > luckily we are already adding that in 3.5 > > see AnalysisAlgorithm in the 3.5 roadmap: > http://www.gusdb.org/wiki/index.php/Gus3.5RoadMap > > steve > > Josef Jurek wrote: > > >Concerning the DoTS.Similarity table which has been discussed > >recently, what we at the Preuss lab are really hurting for > >is a way to distinguish different Blast analyses (different > >blast parameters) of the same subject and query sequences. > >A table as simple as: > > > > id number(10) > > name varchar2(255) > > parameters varchar2(255) > > > >so that one could store something as simple as: > > > > 'Param Set 001' > > '-p blastx -M BLOSUM50 -G 13 -E 2 -e .01 -W 3' > > > >and a way to link these entries to the rows of > >DoTS.Similarity, perhaps in the way that > >DoTS.NASequenceKeyword links rows of DoTS.NASequence > >and DoTS.Keyword, would work. If we were to go ahead and > >add the table to the schema, we might want to actually > >list the parameters individually with a > >comment string, perhaps like: > > > > > > name varchar2(255) > > ... > > expectation_threshold float(22) > > gap_penalty_existence number(10) > > gap_penalty_extension number(10) > > ... > > comment varchar2(255) > > > >Are not other people on the list > >missing the ability to distinguish > >blast results by parameters? > > > >Thanks, Josef > > > > > > > >Josef Jurek, Ph.D. > > > >Daphne Preuss Laboratory > >Molecular Genetics and Cell Biology > >The University of Chicago > >ju...@cs... > > > >voice: (773) 834-3985 > >fax: (773) 702-6648 > > > > |
|
From: Sucheta T. <su...@vb...> - 2005-02-18 13:24:42
|
Hi group, Has anyone upgraded the blast results in the database? If so what is the best way to do that? Many thanks Sucheta -- Sucheta Tripathy Virginia Bioinformatics Institute Phase-I Washington street. Virginia Tech. Blacksburg,VA 24061-0447 phone:(540)231-8138 Fax: (540) 231-2606 |
|
From: <fed...@bi...> - 2005-02-18 09:16:50
|
Thanks everyone! Sorry for not having provided my output; next time all do it! Yes, I'm following fidel and sucheta's guide and as Poliana and Ed suggested my problem was the bootstrap!..I'll tried to update only some row and the output was succesful: today all complete this part! Thanks for help! Federica > federica- > > when you ask for help, it is best to provide the output you see on your > terminal. for example, we don't know what program you were running > from the message below. > > are you following fidel and sucheta's guide? > > steve > > fed...@bi... wrote: > >>Hi guys! I got other troubles! >>I'm inserting new data in DoTS and SRes; both give me the same result >> when >>I run the bash-scripts: >>for DoTS: >>ERROR: Can't update. No row found with primary key sequence_type_id = 1 >>for SRes: >>ERROR: Can't update. No row found with primary key external_database_id >> = 1 >> >>The problem is that it can't update because my table are empty! Is it the >>right condition? And does anyone know how I can solve the >>problem?..Probably before I have to insert data, but how? >>Thanks, >>Federica >> >> >> >>------------------------------------------------------- >>SF email is sponsored by - The IT Product Guide >>Read honest & candid reviews on hundreds of IT Products from real users. >>Discover which products truly live up to the hype. Start reading now. >>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >>_______________________________________________ >>Gusdev-gusdev mailing list >>Gus...@li... >>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> > |
|
From: <ju...@cs...> - 2005-02-17 21:25:54
|
Steve Fischer <sfi...@pc...> writes: > > > we have been discusing ReviewStatus. > [...] > > The immediate action for GUS 3.5 would be: > - name ReviewStatus nullable > - upgrade supported plugins to conform to this proposal > > comments? That all sounds good. That review_status_id should definitely be added to DoTS.NAFeature, is my main concern. Thanks, Josef Josef Jurek, Ph.D. Daphne Preuss Laboratory Molecular Genetics and Cell Biology The University of Chicago ju...@cs... voice: (773) 834-3985 fax: (773) 702-6648 |
|
From: Ed R. <ero...@ug...> - 2005-02-17 21:04:45
|
We need to store much more information in general about algorithm implementations. Even more than parameters, we need information on training sets used, etc. The existing algorithm and algorithmimplementation table do not provide enough detail. Worse, some tables connect to them backwards. Dots.SignalPeptideFeature has a FK link to core.algorithm, not to core.algorithmimplementation, which means there is no way to associate a run of signalP with a version of (1, 2, or 3?). -ed ---- Original message ---- >Date: Thu, 17 Feb 2005 14:55:16 -0600 (CST) >From: ju...@cs..., Josef Jurek <ju...@cs...> >Subject: Re: [Gusdev-gusdev] parseBlastFilesForSimilarity.pl >To: gus...@li... >Cc: ju...@cs... > > >Concerning the DoTS.Similarity table which has been discussed >recently, what we at the Preuss lab are really hurting for >is a way to distinguish different Blast analyses (different >blast parameters) of the same subject and query sequences. >A table as simple as: > > id number(10) > name varchar2(255) > parameters varchar2(255) > >so that one could store something as simple as: > > 'Param Set 001' > '-p blastx -M BLOSUM50 -G 13 -E 2 -e .01 -W 3' > >and a way to link these entries to the rows of >DoTS.Similarity, perhaps in the way that >DoTS.NASequenceKeyword links rows of DoTS.NASequence >and DoTS.Keyword, would work. If we were to go ahead and >add the table to the schema, we might want to actually >list the parameters individually with a >comment string, perhaps like: > > > name varchar2(255) > ... > expectation_threshold float(22) > gap_penalty_existence number(10) > gap_penalty_extension number(10) > ... > comment varchar2(255) > >Are not other people on the list >missing the ability to distinguish >blast results by parameters? > >Thanks, Josef > > > >Josef Jurek, Ph.D. > >Daphne Preuss Laboratory >Molecular Genetics and Cell Biology >The University of Chicago >ju...@cs... > >voice: (773) 834-3985 >fax: (773) 702-6648 > > > > > > > >------------------------------------------------------- >SF email is sponsored by - The IT Product Guide >Read honest & candid reviews on hundreds of IT Products from real users. >Discover which products truly live up to the hype. Start reading now. >http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev ----------------- Ed Robinson Center for Tropical and Emerging Global Diseases University of Georgia, Athens, GA 30602 ero...@ug.../(706)542.1447/254.8883 |
|
From: Steve F. <sfi...@pc...> - 2005-02-17 20:59:20
|
luckily we are already adding that in 3.5 see AnalysisAlgorithm in the 3.5 roadmap: http://www.gusdb.org/wiki/index.php/Gus3.5RoadMap steve Josef Jurek wrote: >Concerning the DoTS.Similarity table which has been discussed >recently, what we at the Preuss lab are really hurting for >is a way to distinguish different Blast analyses (different >blast parameters) of the same subject and query sequences. >A table as simple as: > > id number(10) > name varchar2(255) > parameters varchar2(255) > >so that one could store something as simple as: > > 'Param Set 001' > '-p blastx -M BLOSUM50 -G 13 -E 2 -e .01 -W 3' > >and a way to link these entries to the rows of >DoTS.Similarity, perhaps in the way that >DoTS.NASequenceKeyword links rows of DoTS.NASequence >and DoTS.Keyword, would work. If we were to go ahead and >add the table to the schema, we might want to actually >list the parameters individually with a >comment string, perhaps like: > > > name varchar2(255) > ... > expectation_threshold float(22) > gap_penalty_existence number(10) > gap_penalty_extension number(10) > ... > comment varchar2(255) > >Are not other people on the list >missing the ability to distinguish >blast results by parameters? > >Thanks, Josef > > > >Josef Jurek, Ph.D. > >Daphne Preuss Laboratory >Molecular Genetics and Cell Biology >The University of Chicago >ju...@cs... > >voice: (773) 834-3985 >fax: (773) 702-6648 > > > > > > > >------------------------------------------------------- >SF email is sponsored by - The IT Product Guide >Read honest & candid reviews on hundreds of IT Products from real users. >Discover which products truly live up to the hype. Start reading now. >http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
|
From: <ju...@cs...> - 2005-02-17 20:55:39
|
Concerning the DoTS.Similarity table which has been discussed recently, what we at the Preuss lab are really hurting for is a way to distinguish different Blast analyses (different blast parameters) of the same subject and query sequences. A table as simple as: id number(10) name varchar2(255) parameters varchar2(255) so that one could store something as simple as: 'Param Set 001' '-p blastx -M BLOSUM50 -G 13 -E 2 -e .01 -W 3' and a way to link these entries to the rows of DoTS.Similarity, perhaps in the way that DoTS.NASequenceKeyword links rows of DoTS.NASequence and DoTS.Keyword, would work. If we were to go ahead and add the table to the schema, we might want to actually list the parameters individually with a comment string, perhaps like: name varchar2(255) ... expectation_threshold float(22) gap_penalty_existence number(10) gap_penalty_extension number(10) ... comment varchar2(255) Are not other people on the list missing the ability to distinguish blast results by parameters? Thanks, Josef Josef Jurek, Ph.D. Daphne Preuss Laboratory Molecular Genetics and Cell Biology The University of Chicago ju...@cs... voice: (773) 834-3985 fax: (773) 702-6648 |
|
From: Steve F. <sfi...@pc...> - 2005-02-17 15:25:55
|
federica- when you ask for help, it is best to provide the output you see on your terminal. for example, we don't know what program you were running from the message below. are you following fidel and sucheta's guide? steve fed...@bi... wrote: >Hi guys! I got other troubles! >I'm inserting new data in DoTS and SRes; both give me the same result when >I run the bash-scripts: >for DoTS: >ERROR: Can't update. No row found with primary key sequence_type_id = 1 >for SRes: >ERROR: Can't update. No row found with primary key external_database_id = 1 > >The problem is that it can't update because my table are empty! Is it the >right condition? And does anyone know how I can solve the >problem?..Probably before I have to insert data, but how? >Thanks, >Federica > > > >------------------------------------------------------- >SF email is sponsored by - The IT Product Guide >Read honest & candid reviews on hundreds of IT Products from real users. >Discover which products truly live up to the hype. Start reading now. >http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
|
From: <fed...@bi...> - 2005-02-17 10:19:03
|
Hi guys! I got other troubles! I'm inserting new data in DoTS and SRes; both give me the same result when I run the bash-scripts: for DoTS: ERROR: Can't update. No row found with primary key sequence_type_id = 1 for SRes: ERROR: Can't update. No row found with primary key external_database_id = 1 The problem is that it can't update because my table are empty! Is it the right condition? And does anyone know how I can solve the problem?..Probably before I have to insert data, but how? Thanks, Federica |
|
From: Doma, N. R. \(Contr\) <Nar...@ng...> - 2005-02-16 21:47:48
|
Hi There,
I am new to GUS environment, I am looking for the following information
1. Though the schema is very well designed and self explanatory=20
I would like to have a document which describes all IMP columns and =
tables.
2. would like to get the differences between GUS vs Chado database =
schemas.
Thanks
Narsimha
301-527-0002
|
|
From: <fed...@bi...> - 2005-02-16 14:12:46
|
Thanks a lot!
Federica
> ignore the problems. you don't need those plugins. so don't worry.
>
> steve
>
>
>
> fed...@bi... wrote:
>
>>I'm following the "Fidel and Sucheta's installation guide" and at this
>>moment I'm registering all the Plugin groups. Now I'm working to build
>> the
>>GUS platform. For now I have no other aim.
>>Both GoPlugin and LoadGoAssoc were correctly registered.
>>So what do you think I could do?
>>Federica
>>
>>
>>
>>
>>>federica-
>>>
>>>the problem, i believe, is that these are obsolete plugins.
>>>
>>>GoPlugin and LoadGoAssoc are current.
>>>
>>>I'll see if we can get this directory cleaned up.
>>>
>>>What is it you are trying to do?
>>>
>>>steve
>>>
>>>fed...@bi... wrote:
>>>
>>>
>>>
>>>>Of course!
>>>>
>>>>1) ga +create GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc
>>>>
>>>>ERROR: Can't locate Objects/GUSdev/AASequenceGOFunction.pm in @INC
>>>> (@INC
>>>>contains: /opt/gus_home/lib/perl
>>>>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
>>>>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
>>>>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
>>>>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
>>>>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
>>>>/opt/gus_home/lib/perl/GUS/GOPredict/Plugin/CopyAASeqGoFuncToProtGoFunc.pm
>>>>line 24.
>>>>Compilation failed in require at (eval 3) line 1.
>>>>STACK TRACE
>>>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
>>>>locate Objects/GUSdev/AASequenceGOFunction.pm in @INC ...') called at
>>>>/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
>>>> GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x804d054)','GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc')
>>>>called at /opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>>>line 688
>>>> GUS::PluginMgr::GusApplication::create_or_update_implementation('GUS::PluginMgr::GusApplication=HASH(0x804d054)',0,'GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc')
>>>>called at /opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>>>line 479
>>>> GUS::PluginMgr::GusApplication::doMajorMode_Create('GUS::PluginMgr::GusApplication=HASH(0x804d054)','GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc')
>>>>called at /opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>>>line 289
>>>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d054)','GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc')
>>>>called at /opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>>>line 198
>>>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d054)','ARRAY(0x80606d0)')
>>>>called at /opt/gus_home/bin/ga line 11
>>>>
>>>>2) ga +create GUS::GOPredict::Plugin::DeleteGoPredictions
>>>>
>>>>ERROR: Can't locate Objects/GUSdev/AASequenceGOFunction.pm in @INC
>>>> (@INC
>>>>contains: /opt/gus_home/lib/perl
>>>>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
>>>>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
>>>>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
>>>>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
>>>>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
>>>>/opt/gus_home/lib/perl/GUS/GOPredict/Plugin/DeleteGoPredictions.pm line
>>>>12.
>>>>BEGIN failed--compilation aborted at
>>>>/opt/gus_home/lib/perl/GUS/GOPredict/Plugin/DeleteGoPredictions.pm line
>>>>12.
>>>>Compilation failed in require at (eval 3) line 1.
>>>>STACK TRACE
>>>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
>>>>locate Objects/GUSdev/AASequenceGOFunction.pm in @INC ...') called at
>>>>/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
>>>>
>>>>(..than the same as before)
>>>>
>>>>3) ga +create GUS::GOPredict::Plugin::MakeGoPredictions
>>>>
>>>>ERROR: Can't locate object method "new" via package
>>>>"GUS::GOPredict::Plugin::MakeGoPredictions" at (eval 3) line 1.
>>>>STACK TRACE
>>>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
>>>>locate object method "new" via package "GUS::GOPredict...') called at
>>>>/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
>>>>
>>>>(..than the same as before)
>>>>
>>>>4) ga +create GUS::RAD::Plugin::AnalysisResultLoader
>>>>
>>>>ERROR: Can't locate GUS/Model/RAD3/AssayAnalysis.pm in @INC (@INC
>>>>contains: /opt/gus_home/lib/perl
>>>>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
>>>>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
>>>>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
>>>>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
>>>>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
>>>>/opt/gus_home/lib/perl/GUS/RAD/Plugin/AnalysisResultLoader.pm line 22.
>>>>BEGIN failed--compilation aborted at
>>>>/opt/gus_home/lib/perl/GUS/RAD/Plugin/AnalysisResultLoader.pm line 22.
>>>>Compilation failed in require at (eval 3) line 1.
>>>>STACK TRACE
>>>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
>>>>locate GUS/Model/RAD3/AssayAnalysis.pm in @INC (@INC c...') called at
>>>>/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
>>>>
>>>>(..than the same as before)
>>>>
>>>>5) ga +create GUS::RAD::Plugin::AnalysisResultLoader
>>>>
>>>>ERROR: Can't locate GUS/Model/RAD3/AssayAnalysis.pm in @INC (@INC
>>>>contains: /opt/gus_home/lib/perl
>>>>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
>>>>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
>>>>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
>>>>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
>>>>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
>>>>/opt/gus_home/lib/perl/GUS/RAD/Plugin/AnalysisResultLoader.pm line 22.
>>>>BEGIN failed--compilation aborted at
>>>>/opt/gus_home/lib/perl/GUS/RAD/Plugin/AnalysisResultLoader.pm line 22.
>>>>Compilation failed in require at (eval 3) line 1.
>>>>STACK TRACE
>>>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
>>>>locate GUS/Model/RAD3/AssayAnalysis.pm in @INC (@INC c...') called at
>>>>/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
>>>>
>>>>(..than the same as before)
>>>>
>>>>Thanks, Federica
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>can you send the error messages?
>>>>>
>>>>>thanks
>>>>>steve
>>>>>
>>>>>fed...@bi... wrote:
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>>Hi guys! I'm registering the plugin class name with ga; I had some
>>>>>>problems because ga can't find some perl files:
>>>>>>AASequenceGOFunction.pm,
>>>>>>ArrayControlLoader.pm, AssayAnalysis.pm.
>>>>>>And olso in the MakeGoPredictions plugin I had an error: Can't locate
>>>>>>object method "new" via package
>>>>>>"GUS::GOPredict::Plugin::MakeGoPredictions".
>>>>>>Do you know why?? I think the building process has been correctly
>>>>>>made...
>>>>>>Thanks
>>>>>>Federica
>>>>>>
>>>>>>
>>>>>>
>>>>>>-------------------------------------------------------
>>>>>>SF email is sponsored by - The IT Product Guide
>>>>>>Read honest & candid reviews on hundreds of IT Products from real
>>>>>>users.
>>>>>>Discover which products truly live up to the hype. Start reading now.
>>>>>>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>>>>>>_______________________________________________
>>>>>>Gusdev-gusdev mailing list
>>>>>>Gus...@li...
>>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>-------------------------------------------------------
>>>>>SF email is sponsored by - The IT Product Guide
>>>>>Read honest & candid reviews on hundreds of IT Products from real
>>>>> users.
>>>>>Discover which products truly live up to the hype. Start reading now.
>>>>>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>>>>>_______________________________________________
>>>>>Gusdev-gusdev mailing list
>>>>>Gus...@li...
>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>
>>
>>
>
|
|
From: Steve F. <sfi...@pc...> - 2005-02-16 14:02:37
|
ignore the problems. you don't need those plugins. so don't worry.
steve
fed...@bi... wrote:
>I'm following the "Fidel and Sucheta's installation guide" and at this
>moment I'm registering all the Plugin groups. Now I'm working to build the
>GUS platform. For now I have no other aim.
>Both GoPlugin and LoadGoAssoc were correctly registered.
>So what do you think I could do?
>Federica
>
>
>
>
>>federica-
>>
>>the problem, i believe, is that these are obsolete plugins.
>>
>>GoPlugin and LoadGoAssoc are current.
>>
>>I'll see if we can get this directory cleaned up.
>>
>>What is it you are trying to do?
>>
>>steve
>>
>>fed...@bi... wrote:
>>
>>
>>
>>>Of course!
>>>
>>>1) ga +create GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc
>>>
>>>ERROR: Can't locate Objects/GUSdev/AASequenceGOFunction.pm in @INC (@INC
>>>contains: /opt/gus_home/lib/perl
>>>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
>>>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
>>>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
>>>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
>>>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
>>>/opt/gus_home/lib/perl/GUS/GOPredict/Plugin/CopyAASeqGoFuncToProtGoFunc.pm
>>>line 24.
>>>Compilation failed in require at (eval 3) line 1.
>>>STACK TRACE
>>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
>>>locate Objects/GUSdev/AASequenceGOFunction.pm in @INC ...') called at
>>>/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
>>> GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x804d054)','GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc')
>>>called at /opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>>line 688
>>> GUS::PluginMgr::GusApplication::create_or_update_implementation('GUS::PluginMgr::GusApplication=HASH(0x804d054)',0,'GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc')
>>>called at /opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>>line 479
>>> GUS::PluginMgr::GusApplication::doMajorMode_Create('GUS::PluginMgr::GusApplication=HASH(0x804d054)','GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc')
>>>called at /opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>>line 289
>>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d054)','GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc')
>>>called at /opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>>line 198
>>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d054)','ARRAY(0x80606d0)')
>>>called at /opt/gus_home/bin/ga line 11
>>>
>>>2) ga +create GUS::GOPredict::Plugin::DeleteGoPredictions
>>>
>>>ERROR: Can't locate Objects/GUSdev/AASequenceGOFunction.pm in @INC (@INC
>>>contains: /opt/gus_home/lib/perl
>>>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
>>>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
>>>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
>>>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
>>>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
>>>/opt/gus_home/lib/perl/GUS/GOPredict/Plugin/DeleteGoPredictions.pm line
>>>12.
>>>BEGIN failed--compilation aborted at
>>>/opt/gus_home/lib/perl/GUS/GOPredict/Plugin/DeleteGoPredictions.pm line
>>>12.
>>>Compilation failed in require at (eval 3) line 1.
>>>STACK TRACE
>>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
>>>locate Objects/GUSdev/AASequenceGOFunction.pm in @INC ...') called at
>>>/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
>>>
>>>(..than the same as before)
>>>
>>>3) ga +create GUS::GOPredict::Plugin::MakeGoPredictions
>>>
>>>ERROR: Can't locate object method "new" via package
>>>"GUS::GOPredict::Plugin::MakeGoPredictions" at (eval 3) line 1.
>>>STACK TRACE
>>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
>>>locate object method "new" via package "GUS::GOPredict...') called at
>>>/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
>>>
>>>(..than the same as before)
>>>
>>>4) ga +create GUS::RAD::Plugin::AnalysisResultLoader
>>>
>>>ERROR: Can't locate GUS/Model/RAD3/AssayAnalysis.pm in @INC (@INC
>>>contains: /opt/gus_home/lib/perl
>>>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
>>>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
>>>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
>>>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
>>>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
>>>/opt/gus_home/lib/perl/GUS/RAD/Plugin/AnalysisResultLoader.pm line 22.
>>>BEGIN failed--compilation aborted at
>>>/opt/gus_home/lib/perl/GUS/RAD/Plugin/AnalysisResultLoader.pm line 22.
>>>Compilation failed in require at (eval 3) line 1.
>>>STACK TRACE
>>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
>>>locate GUS/Model/RAD3/AssayAnalysis.pm in @INC (@INC c...') called at
>>>/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
>>>
>>>(..than the same as before)
>>>
>>>5) ga +create GUS::RAD::Plugin::AnalysisResultLoader
>>>
>>>ERROR: Can't locate GUS/Model/RAD3/AssayAnalysis.pm in @INC (@INC
>>>contains: /opt/gus_home/lib/perl
>>>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
>>>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
>>>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
>>>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
>>>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
>>>/opt/gus_home/lib/perl/GUS/RAD/Plugin/AnalysisResultLoader.pm line 22.
>>>BEGIN failed--compilation aborted at
>>>/opt/gus_home/lib/perl/GUS/RAD/Plugin/AnalysisResultLoader.pm line 22.
>>>Compilation failed in require at (eval 3) line 1.
>>>STACK TRACE
>>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
>>>locate GUS/Model/RAD3/AssayAnalysis.pm in @INC (@INC c...') called at
>>>/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
>>>
>>>(..than the same as before)
>>>
>>>Thanks, Federica
>>>
>>>
>>>
>>>
>>>
>>>>can you send the error messages?
>>>>
>>>>thanks
>>>>steve
>>>>
>>>>fed...@bi... wrote:
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>>Hi guys! I'm registering the plugin class name with ga; I had some
>>>>>problems because ga can't find some perl files:
>>>>>AASequenceGOFunction.pm,
>>>>>ArrayControlLoader.pm, AssayAnalysis.pm.
>>>>>And olso in the MakeGoPredictions plugin I had an error: Can't locate
>>>>>object method "new" via package
>>>>>"GUS::GOPredict::Plugin::MakeGoPredictions".
>>>>>Do you know why?? I think the building process has been correctly
>>>>>made...
>>>>>Thanks
>>>>>Federica
>>>>>
>>>>>
>>>>>
>>>>>-------------------------------------------------------
>>>>>SF email is sponsored by - The IT Product Guide
>>>>>Read honest & candid reviews on hundreds of IT Products from real
>>>>>users.
>>>>>Discover which products truly live up to the hype. Start reading now.
>>>>>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>>>>>_______________________________________________
>>>>>Gusdev-gusdev mailing list
>>>>>Gus...@li...
>>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>-------------------------------------------------------
>>>>SF email is sponsored by - The IT Product Guide
>>>>Read honest & candid reviews on hundreds of IT Products from real users.
>>>>Discover which products truly live up to the hype. Start reading now.
>>>>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>>>>_______________________________________________
>>>>Gusdev-gusdev mailing list
>>>>Gus...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>
>
>
|
|
From: <fed...@bi...> - 2005-02-16 13:39:17
|
I'm following the "Fidel and Sucheta's installation guide" and at this
moment I'm registering all the Plugin groups. Now I'm working to build the
GUS platform. For now I have no other aim.
Both GoPlugin and LoadGoAssoc were correctly registered.
So what do you think I could do?
Federica
> federica-
>
> the problem, i believe, is that these are obsolete plugins.
>
> GoPlugin and LoadGoAssoc are current.
>
> I'll see if we can get this directory cleaned up.
>
> What is it you are trying to do?
>
> steve
>
> fed...@bi... wrote:
>
>>Of course!
>>
>>1) ga +create GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc
>>
>>ERROR: Can't locate Objects/GUSdev/AASequenceGOFunction.pm in @INC (@INC
>>contains: /opt/gus_home/lib/perl
>>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
>>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
>>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
>>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
>>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
>>/opt/gus_home/lib/perl/GUS/GOPredict/Plugin/CopyAASeqGoFuncToProtGoFunc.pm
>>line 24.
>>Compilation failed in require at (eval 3) line 1.
>>STACK TRACE
>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
>>locate Objects/GUSdev/AASequenceGOFunction.pm in @INC ...') called at
>>/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
>> GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x804d054)','GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc')
>>called at /opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>line 688
>> GUS::PluginMgr::GusApplication::create_or_update_implementation('GUS::PluginMgr::GusApplication=HASH(0x804d054)',0,'GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc')
>>called at /opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>line 479
>> GUS::PluginMgr::GusApplication::doMajorMode_Create('GUS::PluginMgr::GusApplication=HASH(0x804d054)','GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc')
>>called at /opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>line 289
>> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d054)','GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc')
>>called at /opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>>line 198
>> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d054)','ARRAY(0x80606d0)')
>>called at /opt/gus_home/bin/ga line 11
>>
>>2) ga +create GUS::GOPredict::Plugin::DeleteGoPredictions
>>
>>ERROR: Can't locate Objects/GUSdev/AASequenceGOFunction.pm in @INC (@INC
>>contains: /opt/gus_home/lib/perl
>>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
>>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
>>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
>>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
>>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
>>/opt/gus_home/lib/perl/GUS/GOPredict/Plugin/DeleteGoPredictions.pm line
>>12.
>>BEGIN failed--compilation aborted at
>>/opt/gus_home/lib/perl/GUS/GOPredict/Plugin/DeleteGoPredictions.pm line
>>12.
>>Compilation failed in require at (eval 3) line 1.
>>STACK TRACE
>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
>>locate Objects/GUSdev/AASequenceGOFunction.pm in @INC ...') called at
>>/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
>>
>>(..than the same as before)
>>
>>3) ga +create GUS::GOPredict::Plugin::MakeGoPredictions
>>
>>ERROR: Can't locate object method "new" via package
>>"GUS::GOPredict::Plugin::MakeGoPredictions" at (eval 3) line 1.
>>STACK TRACE
>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
>>locate object method "new" via package "GUS::GOPredict...') called at
>>/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
>>
>>(..than the same as before)
>>
>>4) ga +create GUS::RAD::Plugin::AnalysisResultLoader
>>
>>ERROR: Can't locate GUS/Model/RAD3/AssayAnalysis.pm in @INC (@INC
>>contains: /opt/gus_home/lib/perl
>>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
>>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
>>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
>>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
>>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
>>/opt/gus_home/lib/perl/GUS/RAD/Plugin/AnalysisResultLoader.pm line 22.
>>BEGIN failed--compilation aborted at
>>/opt/gus_home/lib/perl/GUS/RAD/Plugin/AnalysisResultLoader.pm line 22.
>>Compilation failed in require at (eval 3) line 1.
>>STACK TRACE
>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
>>locate GUS/Model/RAD3/AssayAnalysis.pm in @INC (@INC c...') called at
>>/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
>>
>>(..than the same as before)
>>
>>5) ga +create GUS::RAD::Plugin::AnalysisResultLoader
>>
>>ERROR: Can't locate GUS/Model/RAD3/AssayAnalysis.pm in @INC (@INC
>>contains: /opt/gus_home/lib/perl
>>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
>>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
>>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
>>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
>>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
>>/opt/gus_home/lib/perl/GUS/RAD/Plugin/AnalysisResultLoader.pm line 22.
>>BEGIN failed--compilation aborted at
>>/opt/gus_home/lib/perl/GUS/RAD/Plugin/AnalysisResultLoader.pm line 22.
>>Compilation failed in require at (eval 3) line 1.
>>STACK TRACE
>>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
>>locate GUS/Model/RAD3/AssayAnalysis.pm in @INC (@INC c...') called at
>>/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
>>
>>(..than the same as before)
>>
>>Thanks, Federica
>>
>>
>>
>>>can you send the error messages?
>>>
>>>thanks
>>>steve
>>>
>>>fed...@bi... wrote:
>>>
>>>
>>>
>>>>Hi guys! I'm registering the plugin class name with ga; I had some
>>>>problems because ga can't find some perl files:
>>>> AASequenceGOFunction.pm,
>>>>ArrayControlLoader.pm, AssayAnalysis.pm.
>>>>And olso in the MakeGoPredictions plugin I had an error: Can't locate
>>>>object method "new" via package
>>>>"GUS::GOPredict::Plugin::MakeGoPredictions".
>>>>Do you know why?? I think the building process has been correctly
>>>> made...
>>>>Thanks
>>>>Federica
>>>>
>>>>
>>>>
>>>>-------------------------------------------------------
>>>>SF email is sponsored by - The IT Product Guide
>>>>Read honest & candid reviews on hundreds of IT Products from real
>>>> users.
>>>>Discover which products truly live up to the hype. Start reading now.
>>>>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>>>>_______________________________________________
>>>>Gusdev-gusdev mailing list
>>>>Gus...@li...
>>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>>
>>>>
>>>>
>>>>
>>>-------------------------------------------------------
>>>SF email is sponsored by - The IT Product Guide
>>>Read honest & candid reviews on hundreds of IT Products from real users.
>>>Discover which products truly live up to the hype. Start reading now.
>>>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>>
>>
>>
>>
>
|
|
From: Steve F. <sfi...@pc...> - 2005-02-16 12:20:28
|
federica-
the problem, i believe, is that these are obsolete plugins.
GoPlugin and LoadGoAssoc are current.
I'll see if we can get this directory cleaned up.
What is it you are trying to do?
steve
fed...@bi... wrote:
>Of course!
>
>1) ga +create GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc
>
>ERROR: Can't locate Objects/GUSdev/AASequenceGOFunction.pm in @INC (@INC
>contains: /opt/gus_home/lib/perl
>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
>/opt/gus_home/lib/perl/GUS/GOPredict/Plugin/CopyAASeqGoFuncToProtGoFunc.pm
>line 24.
>Compilation failed in require at (eval 3) line 1.
>STACK TRACE
>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
>locate Objects/GUSdev/AASequenceGOFunction.pm in @INC ...') called at
>/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
> GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x804d054)','GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc')
>called at /opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 688
> GUS::PluginMgr::GusApplication::create_or_update_implementation('GUS::PluginMgr::GusApplication=HASH(0x804d054)',0,'GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc')
>called at /opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 479
> GUS::PluginMgr::GusApplication::doMajorMode_Create('GUS::PluginMgr::GusApplication=HASH(0x804d054)','GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc')
>called at /opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 289
> GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d054)','GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc')
>called at /opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
>line 198
> GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d054)','ARRAY(0x80606d0)')
>called at /opt/gus_home/bin/ga line 11
>
>2) ga +create GUS::GOPredict::Plugin::DeleteGoPredictions
>
>ERROR: Can't locate Objects/GUSdev/AASequenceGOFunction.pm in @INC (@INC
>contains: /opt/gus_home/lib/perl
>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
>/opt/gus_home/lib/perl/GUS/GOPredict/Plugin/DeleteGoPredictions.pm line
>12.
>BEGIN failed--compilation aborted at
>/opt/gus_home/lib/perl/GUS/GOPredict/Plugin/DeleteGoPredictions.pm line
>12.
>Compilation failed in require at (eval 3) line 1.
>STACK TRACE
>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
>locate Objects/GUSdev/AASequenceGOFunction.pm in @INC ...') called at
>/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
>
>(..than the same as before)
>
>3) ga +create GUS::GOPredict::Plugin::MakeGoPredictions
>
>ERROR: Can't locate object method "new" via package
>"GUS::GOPredict::Plugin::MakeGoPredictions" at (eval 3) line 1.
>STACK TRACE
>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
>locate object method "new" via package "GUS::GOPredict...') called at
>/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
>
>(..than the same as before)
>
>4) ga +create GUS::RAD::Plugin::AnalysisResultLoader
>
>ERROR: Can't locate GUS/Model/RAD3/AssayAnalysis.pm in @INC (@INC
>contains: /opt/gus_home/lib/perl
>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
>/opt/gus_home/lib/perl/GUS/RAD/Plugin/AnalysisResultLoader.pm line 22.
>BEGIN failed--compilation aborted at
>/opt/gus_home/lib/perl/GUS/RAD/Plugin/AnalysisResultLoader.pm line 22.
>Compilation failed in require at (eval 3) line 1.
>STACK TRACE
>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
>locate GUS/Model/RAD3/AssayAnalysis.pm in @INC (@INC c...') called at
>/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
>
>(..than the same as before)
>
>5) ga +create GUS::RAD::Plugin::AnalysisResultLoader
>
>ERROR: Can't locate GUS/Model/RAD3/AssayAnalysis.pm in @INC (@INC
>contains: /opt/gus_home/lib/perl
>/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
>/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
>/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
>/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
>/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
>/opt/gus_home/lib/perl/GUS/RAD/Plugin/AnalysisResultLoader.pm line 22.
>BEGIN failed--compilation aborted at
>/opt/gus_home/lib/perl/GUS/RAD/Plugin/AnalysisResultLoader.pm line 22.
>Compilation failed in require at (eval 3) line 1.
>STACK TRACE
>GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
>locate GUS/Model/RAD3/AssayAnalysis.pm in @INC (@INC c...') called at
>/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
>
>(..than the same as before)
>
>Thanks, Federica
>
>
>
>>can you send the error messages?
>>
>>thanks
>>steve
>>
>>fed...@bi... wrote:
>>
>>
>>
>>>Hi guys! I'm registering the plugin class name with ga; I had some
>>>problems because ga can't find some perl files: AASequenceGOFunction.pm,
>>>ArrayControlLoader.pm, AssayAnalysis.pm.
>>>And olso in the MakeGoPredictions plugin I had an error: Can't locate
>>>object method "new" via package
>>>"GUS::GOPredict::Plugin::MakeGoPredictions".
>>>Do you know why?? I think the building process has been correctly made...
>>>Thanks
>>>Federica
>>>
>>>
>>>
>>>-------------------------------------------------------
>>>SF email is sponsored by - The IT Product Guide
>>>Read honest & candid reviews on hundreds of IT Products from real users.
>>>Discover which products truly live up to the hype. Start reading now.
>>>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>>>_______________________________________________
>>>Gusdev-gusdev mailing list
>>>Gus...@li...
>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
>>>
>>>
>>-------------------------------------------------------
>>SF email is sponsored by - The IT Product Guide
>>Read honest & candid reviews on hundreds of IT Products from real users.
>>Discover which products truly live up to the hype. Start reading now.
>>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>>
>
>
>
|
|
From: <fed...@bi...> - 2005-02-16 08:47:32
|
Of course!
1) ga +create GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc
ERROR: Can't locate Objects/GUSdev/AASequenceGOFunction.pm in @INC (@INC
contains: /opt/gus_home/lib/perl
/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
/opt/gus_home/lib/perl/GUS/GOPredict/Plugin/CopyAASeqGoFuncToProtGoFunc.pm
line 24.
Compilation failed in require at (eval 3) line 1.
STACK TRACE
GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
locate Objects/GUSdev/AASequenceGOFunction.pm in @INC ...') called at
/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
GUS::PluginMgr::GusApplication::newFromPluginName('GUS::PluginMgr::GusApplication=HASH(0x804d054)','GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc')
called at /opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 688
GUS::PluginMgr::GusApplication::create_or_update_implementation('GUS::PluginMgr::GusApplication=HASH(0x804d054)',0,'GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc')
called at /opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 479
GUS::PluginMgr::GusApplication::doMajorMode_Create('GUS::PluginMgr::GusApplication=HASH(0x804d054)','GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc')
called at /opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 289
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x804d054)','GUS::GOPredict::Plugin::CopyAASeqGoFuncToProtGoFunc')
called at /opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm
line 198
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x804d054)','ARRAY(0x80606d0)')
called at /opt/gus_home/bin/ga line 11
2) ga +create GUS::GOPredict::Plugin::DeleteGoPredictions
ERROR: Can't locate Objects/GUSdev/AASequenceGOFunction.pm in @INC (@INC
contains: /opt/gus_home/lib/perl
/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
/opt/gus_home/lib/perl/GUS/GOPredict/Plugin/DeleteGoPredictions.pm line
12.
BEGIN failed--compilation aborted at
/opt/gus_home/lib/perl/GUS/GOPredict/Plugin/DeleteGoPredictions.pm line
12.
Compilation failed in require at (eval 3) line 1.
STACK TRACE
GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
locate Objects/GUSdev/AASequenceGOFunction.pm in @INC ...') called at
/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
(..than the same as before)
3) ga +create GUS::GOPredict::Plugin::MakeGoPredictions
ERROR: Can't locate object method "new" via package
"GUS::GOPredict::Plugin::MakeGoPredictions" at (eval 3) line 1.
STACK TRACE
GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
locate object method "new" via package "GUS::GOPredict...') called at
/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
(..than the same as before)
4) ga +create GUS::RAD::Plugin::AnalysisResultLoader
ERROR: Can't locate GUS/Model/RAD3/AssayAnalysis.pm in @INC (@INC
contains: /opt/gus_home/lib/perl
/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
/opt/gus_home/lib/perl/GUS/RAD/Plugin/AnalysisResultLoader.pm line 22.
BEGIN failed--compilation aborted at
/opt/gus_home/lib/perl/GUS/RAD/Plugin/AnalysisResultLoader.pm line 22.
Compilation failed in require at (eval 3) line 1.
STACK TRACE
GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
locate GUS/Model/RAD3/AssayAnalysis.pm in @INC (@INC c...') called at
/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
(..than the same as before)
5) ga +create GUS::RAD::Plugin::AnalysisResultLoader
ERROR: Can't locate GUS/Model/RAD3/AssayAnalysis.pm in @INC (@INC
contains: /opt/gus_home/lib/perl
/usr/lib/perl5/5.8.0/i386-linux-thread-multi /usr/lib/perl5/5.8.0
/usr/lib/perl5/site_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.0 /usr/lib/perl5/site_perl
/usr/lib/perl5/vendor_perl/5.8.0/i386-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.0 /usr/lib/perl5/vendor_perl .) at
/opt/gus_home/lib/perl/GUS/RAD/Plugin/AnalysisResultLoader.pm line 22.
BEGIN failed--compilation aborted at
/opt/gus_home/lib/perl/GUS/RAD/Plugin/AnalysisResultLoader.pm line 22.
Compilation failed in require at (eval 3) line 1.
STACK TRACE
GUS::PluginMgr::Plugin::error('GUS::PluginMgr::GusApplication=HASH(0x804d054)','Can\'t
locate GUS/Model/RAD3/AssayAnalysis.pm in @INC (@INC c...') called at
/opt/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 254
(..than the same as before)
Thanks, Federica
> can you send the error messages?
>
> thanks
> steve
>
> fed...@bi... wrote:
>
>>Hi guys! I'm registering the plugin class name with ga; I had some
>>problems because ga can't find some perl files: AASequenceGOFunction.pm,
>>ArrayControlLoader.pm, AssayAnalysis.pm.
>>And olso in the MakeGoPredictions plugin I had an error: Can't locate
>>object method "new" via package
>>"GUS::GOPredict::Plugin::MakeGoPredictions".
>>Do you know why?? I think the building process has been correctly made...
>>Thanks
>>Federica
>>
>>
>>
>>-------------------------------------------------------
>>SF email is sponsored by - The IT Product Guide
>>Read honest & candid reviews on hundreds of IT Products from real users.
>>Discover which products truly live up to the hype. Start reading now.
>>http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
>>_______________________________________________
>>Gusdev-gusdev mailing list
>>Gus...@li...
>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>>
>
>
> -------------------------------------------------------
> SF email is sponsored by - The IT Product Guide
> Read honest & candid reviews on hundreds of IT Products from real users.
> Discover which products truly live up to the hype. Start reading now.
> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: Sucheta T. <su...@vb...> - 2005-02-15 18:39:53
|
Steve, You are right, parent_ids are there for some of them, but some others like transcript does not have one. I feel a parent_id needs to be there for transcript rather than genefeature. Since a transcript is derived from a gene. sucheta > sucheta- > > i *think* the answer to your question may be that features have > parent_id. this is used to build feature trees. > > steve > > Sucheta Tripathy wrote: > >> Thank you all for the response. My original question was bit premature >> and based on more of our convenience than the design of GUS per se. >> >> But these are some issues, I think the group may need to consider: >> >> By keeping different prediction outputs as different feature_ids and >> finally merging them through gene and gene_instance seems fine. But we >> need to distinguish between features within a gene and features of a >> gene. What I mean by that is a gene may have different features like >> an UTR feature , a promoter element feature etc, a cpg island feature >> and so on. which needs to be linked to a particular prediction output. >> >> For example I have gene 1 with gene_id 1 which has several >> gene_instances represented by different prediction algorithms and each >> having a different na_feature_id say: 1,2,3,4. >> >> For prediction algorithm with na_feature_id=1, I have a set of UTR >> locations and say I have feature_id 5 for UTR_5 and 6 for UTR_3 and a >> promoter feature with na_feature_id 7. Then how would I link >> na_feature_ids 1,5,6 and 7. >> >> So, for this I was thinking if one na_feature_id could represent a >> gene and its locations could have a description each with reviewer's >> status etc. And to save the geneinstances for any kind of splice >> variants or any other types of instances. >> >> Many thanks >> >> Sucheta >> >> At 09:40 AM 2/14/2005 -0500, you wrote: >> >>> This question is a bit more complex than it seems. >>> >>> All three of these may be necessary for every level of >>> analysis. first, was the overall gene prediction/feature >>> prediction reviewed and how was it algorithmically arrived at? >>> Then you can ask the same question about the locations. >>> Early locations may be provided by the same algorithm as the >>> feature, but these may be further defined later and require >>> their own review annotations. >>> >>> One thing that I think needs to be addressed, however, is how >>> these columns appear throughout the schema like mushrooms. I >>> have been told that GUS was hyper-normalized when it was first >>> written to 4N or 5N form, but that is definitely not the case >>> now. Why do you want review_status, reviewer and algorithm in >>> the feature table? Since these usually will appear in >>> clusters (i.e. running an algorithm once gives you 500 cases >>> of the same entry for all three on the same date), shouldn't >>> we have a table to collect these into an annotation_status >>> table and just have an FK to an entry in that table for every >>> table that uses these? The same goes for other SRes entries >>> such as taxon, project, etc. >>> >>> -Ed >>> >>> >>> >>> ---- Original message ---- >>> >Date: Sat, 12 Feb 2005 22:34:03 -0500 (EST) >>> >From: "Sucheta Tripathy" <su...@vb...> >>> >Subject: [Gusdev-gusdev] dots.nalocation table >>> >To: Gus...@li... >>> > >>> > >>> >Hi Group, >>> > >>> >From community annotation point of view, I was wondering if >>> it is a good >>> >idea to have is_reviewed, algorithm_id and reviewer_id in >>> dots.nalocation >>> >table. >>> > >>> >Since one na_feature_id( a transcript or a gene) may be >>> having multiple >>> >sets of nalocations, so one can easily capture them in >>> nalocation with >>> >different algorithms and with a reviewed option. >>> > >>> >In our application we need several gene calling programs to >>> have locations >>> >as well as related information registered. >>> > >>> >Sucheta >>> > >>> > >>> >-- >>> >Sucheta Tripathy >>> >Virginia Bioinformatics Institute Phase-I >>> >Washington street. >>> >Virginia Tech. >>> >Blacksburg,VA 24061-0447 >>> >phone:(540)231-8138 >>> >Fax: (540) 231-2606 >>> > >>> > >>> >------------------------------------------------------- >>> >SF email is sponsored by - The IT Product Guide >>> >Read honest & candid reviews on hundreds of IT Products from >>> real users. >>> >Discover which products truly live up to the hype. Start >>> reading now. >>> >http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >>> >_______________________________________________ >>> >Gusdev-gusdev mailing list >>> >Gus...@li... >>> >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>> ----------------- >>> Ed Robinson >>> Center for Tropical and Emerging Global Diseases >>> University of Georgia, Athens, GA 30602 >>> ero...@ug.../(706)542.1447/254.8883 >>> >>> >>> ------------------------------------------------------- >>> SF email is sponsored by - The IT Product Guide >>> Read honest & candid reviews on hundreds of IT Products from real >>> users. >>> Discover which products truly live up to the hype. Start reading now. >>> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >>> _______________________________________________ >>> Gusdev-gusdev mailing list >>> Gus...@li... >>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> >> >> >> ------------------------------------------------------- >> SF email is sponsored by - The IT Product Guide >> Read honest & candid reviews on hundreds of IT Products from real users. >> Discover which products truly live up to the hype. Start reading now. >> http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > ------------------------------------------------------- > SF email is sponsored by - The IT Product Guide > Read honest & candid reviews on hundreds of IT Products from real users. > Discover which products truly live up to the hype. Start reading now. > http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > -- Sucheta Tripathy Virginia Bioinformatics Institute Phase-I Washington street. Virginia Tech. Blacksburg,VA 24061-0447 phone:(540)231-8138 Fax: (540) 231-2606 |
|
From: Steve F. <sfi...@pc...> - 2005-02-15 18:27:41
|
can you send the error messages? thanks steve fed...@bi... wrote: >Hi guys! I'm registering the plugin class name with ga; I had some >problems because ga can't find some perl files: AASequenceGOFunction.pm, >ArrayControlLoader.pm, AssayAnalysis.pm. >And olso in the MakeGoPredictions plugin I had an error: Can't locate >object method "new" via package >"GUS::GOPredict::Plugin::MakeGoPredictions". >Do you know why?? I think the building process has been correctly made... >Thanks >Federica > > > >------------------------------------------------------- >SF email is sponsored by - The IT Product Guide >Read honest & candid reviews on hundreds of IT Products from real users. >Discover which products truly live up to the hype. Start reading now. >http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
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