gusdev-gusdev — Topics concerning GUS development

[GUSDEV] genes with more than one EC number

[Fernan A. <fe...@ii...>]

Hi,

we're having problems loading files where genes have more
than one EC number (we're using the supported
InsertSequenceFeatures plugin). 

Depending on how you view the problem it could be an issue
of the plugin, the underlying schema, or both.

Given that it is not unexpected that proteins could have
more than one EC number, this should not be the standard
behaviour (maybe give a warning but still continue loading?).

Is this a known bug? Anyone has already worked around this?

If not, I'll be submitting an issue to the tracker,

Fernan

Re: [GUSDEV] Gusdev-gusdev Digest, Vol 4, Issue 3

[<mro...@cs...>]

Steve,

I am sure that I am NOT using the "build command to get my files from
project_home to gus_home" because I do not what you are talking about,
could you please tell me how to run that command.

Then if I still have a problem I will replace $Revision$ in the plugin
file with a number like 5023

I hope you are enjoying some great pasta and pizza

Thank you very much

Michael

Re: [GUSDEV] InsertSequenceFeatures.pm

[<sfi...@pc...>]

michael-

our file server is down and i'm in italy, so i'm working a bit in the dark.

i don't know why the file you are getting from the svn site doesn't have the
revision correctly.  you need to replace $Revision$ in the plugin file with a
number like 5023

also, are you using the build command to get your files from project_home to
gus_home?

steve

Quoting mro...@cs...:

> Steve,
>
> Thank you very much for your help, here is the complete situation as of
> today.
>
>
> 1 - The data that i am trying to load into gus is Pseudomonas_aeruginosa"
> found at
>
> ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Pseudomonas_aeruginosa/
>
>
> 2 - today I run (using revision 1000)
> ga GUS::Supported::Plugin::InsertSequenceFeatures
> --mapFile $HOME/"pseudomonas aeruginosa"/pa01/genbank2gus.xml
> --inputFileOrDir $HOME/"pseudomonas aeruginosa"/pa01/NC_002516.gbk
> --fileFormat genbank
> --extDbName "Pseudomonas_aeruginosa"
> --extDbRlsVer "1000"
> --soCvsVersion "1.41"
> --commit
>
> and I get the same error as before:
>
> The plugin has an illegal cvs revision: '$Revision$'.  If that doesn't
> include a revision number, then the plugin has never been checked into
> CVS. Please do so to give it an intial revision at /home/acrl-storage-
> 1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 347.
> Database handle destroyed without explicit disconnect.
>
>
> 3 - today I realized that I needed to do
>
> ga +create GUS::Supported::Plugin::InsertSequenceFeatures
>
> and I get the same error as above
>
> The plugin has an illegal cvs revision: '$Revision$'.  If that doesn't
> include a revision number, then the plugin has never been checked into
> CVS. Please do so to give it an intial revision at /home/acrl-storage-
> 1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 347.
>
>
> 4 - I found "InsertSequenceFeatures.pm" and the following plugins at:
>
> https://www.cbil.upenn.edu/svn/gus/GusAppFramework/trunk/Supported/plugin/perl/
>
> Revision 5023: /GusAppFramework/trunk/Supported/plugin/perl
> ..
> CalculateAASequenceMolWt.pm
> CalculateTranslatedAASequences.pm
> ExtractTranscriptSequences.pm
> InsertArrayDesignControl.pm
> InsertAssayControl.pm
> InsertBlastSimilarities.pm
> InsertExternalDatabase.pm
> InsertExternalDatabaseRls.pm
> InsertGOEvidenceCode.pm
> InsertGene2Accession.pm
> InsertGene2Go.pm
> InsertGeneOntology.pm
> InsertGeneOntologyAssoc.pm
> InsertHomoloGene.pm
> InsertOntologyEntry.pm
> InsertOntologyRelationshipType.pm
> InsertOntologyTermType.pm
> InsertOntologyTermsAndRelationships.pm
> InsertRadAnalysis.pm
> InsertReviewStatus.pm
> InsertSecondaryStructure.pm
> InsertSequenceFeatures.pm
> InsertSequenceFeaturesUndo.pm
> InsertSequenceOntology.pm
> InsertSequenceOntologyNew.pm
> InsertSequenceOntologyOBO.pm
> InsertTandemRepeatFeatures.pm
> InsertTaxonAndTaxonName.pm
> LoadArrayDesign.pm
> LoadArrayResults.pm
> LoadFastaSequences.pm
> LoadGusXml.pm
> LoadNRDB.pm
> LoadRow.pm
> LoadTaxon.pm
> dbEST.pm
>
> since they were NOT at
>
> /home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/Supported/Plugin
>
> I added them to that directory
>
> Then I executed InsertSequenceFeatures.pm  --help and it worked,
>
>
> At this time I am comming to the conclusion that just copying the missing
> plugins into the
> "/home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/Supported/Plugin"
> directory is not enough since the error talks about
>
> "the plugin has never been checked into CVS. Please do so to give it an
> intial revision at
> /home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/Plugin.pm
> line 347."
>
> if i am correct, how can i check all the above plugins into CVS, and is
> there something else that I need to do?
>
>
>
> Thank you very much for your help
>
>
>
> Michael Robinson
> Bioinformatics Research Group (Biorg)
> Florida International University
> Miami, Florida, USA 33199
>
>
>
>
>
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>

[GUSDEV] InsertSequenceFeatures.pm

[<mro...@cs...>]

Steve,

Thank you very much for your help, here is the complete situation as of
today.


1 - The data that i am trying to load into gus is Pseudomonas_aeruginosa"
found at

ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Pseudomonas_aeruginosa/


2 - today I run (using revision 1000)
ga GUS::Supported::Plugin::InsertSequenceFeatures
--mapFile $HOME/"pseudomonas aeruginosa"/pa01/genbank2gus.xml
--inputFileOrDir $HOME/"pseudomonas aeruginosa"/pa01/NC_002516.gbk
--fileFormat genbank
--extDbName "Pseudomonas_aeruginosa"
--extDbRlsVer "1000"
--soCvsVersion "1.41"
--commit

and I get the same error as before:

The plugin has an illegal cvs revision: '$Revision$'.  If that doesn't
include a revision number, then the plugin has never been checked into
CVS. Please do so to give it an intial revision at /home/acrl-storage-
1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 347.
Database handle destroyed without explicit disconnect.


3 - today I realized that I needed to do

ga +create GUS::Supported::Plugin::InsertSequenceFeatures

and I get the same error as above

The plugin has an illegal cvs revision: '$Revision$'.  If that doesn't
include a revision number, then the plugin has never been checked into
CVS. Please do so to give it an intial revision at /home/acrl-storage-
1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/Plugin.pm line 347.


4 - I found "InsertSequenceFeatures.pm" and the following plugins at:

https://www.cbil.upenn.edu/svn/gus/GusAppFramework/trunk/Supported/plugin=
/perl/

Revision 5023: /GusAppFramework/trunk/Supported/plugin/perl
..
CalculateAASequenceMolWt.pm
CalculateTranslatedAASequences.pm
ExtractTranscriptSequences.pm
InsertArrayDesignControl.pm
InsertAssayControl.pm
InsertBlastSimilarities.pm
InsertExternalDatabase.pm
InsertExternalDatabaseRls.pm
InsertGOEvidenceCode.pm
InsertGene2Accession.pm
InsertGene2Go.pm
InsertGeneOntology.pm
InsertGeneOntologyAssoc.pm
InsertHomoloGene.pm
InsertOntologyEntry.pm
InsertOntologyRelationshipType.pm
InsertOntologyTermType.pm
InsertOntologyTermsAndRelationships.pm
InsertRadAnalysis.pm
InsertReviewStatus.pm
InsertSecondaryStructure.pm
InsertSequenceFeatures.pm
InsertSequenceFeaturesUndo.pm
InsertSequenceOntology.pm
InsertSequenceOntologyNew.pm
InsertSequenceOntologyOBO.pm
InsertTandemRepeatFeatures.pm
InsertTaxonAndTaxonName.pm
LoadArrayDesign.pm
LoadArrayResults.pm
LoadFastaSequences.pm
LoadGusXml.pm
LoadNRDB.pm
LoadRow.pm
LoadTaxon.pm
dbEST.pm

since they were NOT at

/home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/Supported/Plugin

I added them to that directory

Then I executed InsertSequenceFeatures.pm  --help and it worked,


At this time I am comming to the conclusion that just copying the missing
plugins into the
"/home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/Supported/Plugin"
directory is not enough since the error talks about

"the plugin has never been checked into CVS. Please do so to give it an
intial revision at
/home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/Plugin.pm
line 347."

if i am correct, how can i check all the above plugins into CVS, and is
there something else that I need to do?



Thank you very much for your help



Michael Robinson
Bioinformatics Research Group (Biorg)
Florida International University
Miami, Florida, USA 33199

Re: [GUSDEV] Gusdev-gusdev Digest, Vol 3, Issue 4

[<mro...@cs...>]

Good afternoon;

I am trying to run:

ga GUS::Supported::Plugin::InsertSequenceFeatures
--mapFile $HOME/"pseudomonas aeruginosa"/pa01/genbank2gus.xml
--inputFileOrDir $HOME/"pseudomonas aeruginosa"/pa01/NC_002516.gbk
--fileFormat genbank
--extDbName "Pseudomonas_aeruginosa"
--extDbRlsVer "06-16-2006"
--soCvsVersion "1.41"
--commit

and I get the following error:

 The plugin has an illegal cvs revision: '$Revision$'.
 If that doesn't include a revision number, then the plugin has never bee=
n
 checked into CVS.
 Please do so to give it an intial revision at
 /home/acrl-storage-1/gusdb/GUS/gus_home/lib/perl/GUS/PluginMgr/Plugin.pm
 line 347.
 Database handle destroyed without explicit disconnect.


Line 347 of Plugin.pm has the following code:

 $self->{cvsRevision} =3D~ /Revision:\s+(\S+)\s+/ || die "The plugin has =
an
 illegal cvs revision: '$self->{cvsRevision}'.  If that doesn't include a
 revision number, then the plugin has never been checked into CVS.  Pleas=
e
 do so to give it an intial revision";
  return $1;


I have been searching the "archive emails" but I have not been able to
find how to "check the plugin into CVS".


Any help will very much appreciated.


Michael Robinson
Bioinformatics Research Group (Biorg)
Florida International University
Miami, Florida, USA 33199

[GUSDEV] (relatively) recent presentations on GUS

[Chris S. <sto...@pc...>]

Hi All,
Have just posted a powerpoint presentations on GUS at http:// 
www.cbil.upenn.edu/downloads/GUS/documentation/

You can get there from the the "informal notes and presentations"  
link in the Other Resources section at the bottom of
http://www.gusdb.org/documentation.php

BRCGUS06.ppt : Mini workshop on GUS for the Bioinformatics Resource  
Center retreat in Philadelphia (Feb 06).

Cheers,
Chris

Chris Stoeckert, Ph.D.
Research Associate Professor, Dept. of Genetics
1415 Blockley Hall, Center for Bioinformatics
423 Guardian Dr., University of Pennsylvania
Philadelphia, PA 19104
Ph: 215-573-4409 FAX: 215-573-3111

Re: [GUSDEV] Incomplete generation of child relations from FK on PostgreSQL

[John I. <io...@pc...>]

Dr. Galea,

Thank you for finding this solution.  I'll test it and check it in to  
the repository.  This will take a little while, since I'll have to  
install PostgreSQL and GUS.  But that will be a good thing to have.

John Iodice
Computational Biology and Informatics Lab


On Aug 18, 2006, at 9:19 AM, an...@ne... wrote:

> Hello all,
> I've stumbled upon a bug in the PostgreSQL implementation of the  
> Perl object
> layer: when generating Perl objects, most childRelations are  
> missing even if
> the PostgreSQL database contains the relevant FK constraint.
>
> The same bug shows up on two different PostgreSQL versions, namely  
> 8.1.4 and
> 7.4.13.
>
> The problem lies in file '$PROJECT_HOME/GUS/ObjRelP/lib/perl/ 
> PostgreSQL.pm':
> the subroutine 'tableChildRelationsSql' returns incorrect (schema  
> names are
> reversed) and incomplete (filtering by schema name discards  
> relations to
> external schemas) data.
>
> I'm attaching a file 'query.pl' that shows the problem on child  
> relations for
> table 'GUS::Model::SRes::Contact', and a modified version of  
> PostgreSQL.pm with
> a query that works correctly for me.
>
> Here is the output with the original query:
>
> TABLE GUS::Model::SRes::Contact
> ---- Child relations from $db->getTableChildRelations
> GUS::Model::SRes::BibliographicReference, contact_id, contact_id
> GUS::Model::SRes::Contact, contact_id, affiliation_id
> ------------
>
> While this is the output with the modified SQL (incidentally, this  
> very same
> output should be what is obtained from a working installation on  
> Oracle):
>
> TABLE GUS::Model::SRes::Contact
> ---- Child relations from $db->getTableChildRelations
> GUS::Model::Core::UserInfo, contact_id, contact_id
> GUS::Model::DoTS::AASequenceEnzymeClass, contact_id,  
> ec_assignment_contact_id
> GUS::Model::DoTS::Attribution, contact_id, contact_id
> GUS::Model::DoTS::CloneSet, contact_id, contact_id
> GUS::Model::DoTS::EST, contact_id, contact_id
> GUS::Model::DoTS::NASequenceImp, contact_id,  
> sequencing_center_contact_id
> GUS::Model::RAD::Analysis, contact_id, operator_id
> GUS::Model::RAD::ArrayDesign, contact_id, manufacturer_id
> GUS::Model::RAD::Assay, contact_id, operator_id
> GUS::Model::RAD::Quantification, contact_id, operator_id
> GUS::Model::SRes::BibliographicReference, contact_id, contact_id
> GUS::Model::SRes::Contact, contact_id, affiliation_id
> GUS::Model::Study::BioMaterialImp, contact_id, bio_source_provider_id
> GUS::Model::Study::Study, contact_id, contact_id
> ------------
>
> Is there anyone using GUSDB on PostgreSQL who can confirm this  
> issue and test
> that my solution does not break anything else?
>
> Thanks a lot in advance,
>
> Antonio Galea
>
>
>
> ----------------------------------------------------------------
> Net Wise webmail system - http://www.netwise.it
> This message was sent using IMP, the Internet Messaging Program.
> <PostgreSQL.pm>
> <query.pl>

Re: [GUSDEV] Description of tables - documentation

[Chris S. <sto...@pc...>]

Since Steve answered the others ...
>> 4- Table NALocation
>> LOC_ORDER
A feature (e.g., RNA, Gene) can have multiple locations on a  
sequence  (e.g., contig, virtual sequence). This tells you the order  
of those multiple locations although it may be inferred from the  
starts and ends.

>> IS_EXCLUDED
don't remember offhand ..

>> DB_NAME
>> DB_IDENTIFIER
probably should be database_release_id and source_id

>> LITERAL_SEQUENCE
again don't really remember but think it may be for helping specify  
the sequence the location marks by literally providing it

>> REMARK
comment field
>>
>> DEBUG_FIELD
I'm guessing another type of comment field

Chris

On Aug 18, 2006, at 9:47 AM, Steve Fischer wrote:

> ok, see below
>
> Ana Carol wrote:
>> Hello all!
>>
>> I need to know the description/definition of some terms that don't  
>> have in
>> gus schema browser.
>> Can you help me???
>> 1- Table NASequence
>> SEQUENCE_PIECE_ID
>>
> this is a foreign key to the SequencePiece view.  this is used to tie
> together pieces of sequence into a virtual sequence.  the real-world
> application is to model scaffolds.
>> 2- Table Similarity
>> BIT_SCORE_SUMMARY
>>
> this is designed to hold the bit score summary provided in a BLAST
> result.  it summarizes all the bit scores of the individual HSPs
>> 3- Table SimilaritySpan
>> BIT_SCORE
>>
> a bit score of a BLAST HSP
>> 4- Table NALocation
>> LOC_ORDER
>> IS_EXCLUDED
>> DB_NAME
>> DB_IDENTIFIER
>> LITERAL_SEQUENCE
>> REMARK
>> DEBUG_FIELD
>>
> i don't know....  i say ignore these, if you can.
>> 5- Table NAProtein/NAGene
>> IS_VERIFIED
>>
> this is set to 1 if a curator has reviewed the protein or gene
>> I need this to put in my final dissertation of master's degree and  
>> i don't
>> know biology very well, but I studied GUS more or less...
>>
>> Thanks in advance,
>> Ana Carolina
>>
>>
>>
>> --------------------------------------------------------------------- 
>> ---
>>
>> --------------------------------------------------------------------- 
>> ----
>> Using Tomcat but need to do more? Need to support web services,  
>> security?
>> Get stuff done quickly with pre-integrated technology to make your  
>> job easier
>> Download IBM WebSphere Application Server v.1.0.1 based on Apache  
>> Geronimo
>> http://sel.as-us.falkag.net/sel? 
>> cmd=lnk&kid=120709&bid=263057&dat=121642
>> --------------------------------------------------------------------- 
>> ---
>>
>> _______________________________________________
>> Gusdev-gusdev mailing list
>> Gus...@li...
>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>
> ---------------------------------------------------------------------- 
> ---
> Using Tomcat but need to do more? Need to support web services,  
> security?
> Get stuff done quickly with pre-integrated technology to make your  
> job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache  
> Geronimo
> http://sel.as-us.falkag.net/sel? 
> cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev

Re: [GUSDEV] Description of tables - documentation

[Steve F. <sfi...@pc...>]

ok, see below

Ana Carol wrote:
> Hello all! 
>
> I need to know the description/definition of some terms that don't have in 
> gus schema browser. 
> Can you help me??? 
> 1- Table NASequence 
> SEQUENCE_PIECE_ID 
>   
this is a foreign key to the SequencePiece view.  this is used to tie 
together pieces of sequence into a virtual sequence.  the real-world 
application is to model scaffolds.
> 2- Table Similarity 
> BIT_SCORE_SUMMARY 
>   
this is designed to hold the bit score summary provided in a BLAST 
result.  it summarizes all the bit scores of the individual HSPs
> 3- Table SimilaritySpan 
> BIT_SCORE 
>   
a bit score of a BLAST HSP
> 4- Table NALocation 
> LOC_ORDER 
> IS_EXCLUDED 
> DB_NAME 
> DB_IDENTIFIER 
> LITERAL_SEQUENCE 
> REMARK 
> DEBUG_FIELD 
>   
i don't know....  i say ignore these, if you can. 
> 5- Table NAProtein/NAGene 
> IS_VERIFIED 
>   
this is set to 1 if a curator has reviewed the protein or gene
> I need this to put in my final dissertation of master's degree and i don't 
> know biology very well, but I studied GUS more or less... 
>
> Thanks in advance, 
> Ana Carolina 
>
>
>   
> ------------------------------------------------------------------------
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> ------------------------------------------------------------------------
>
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>   

[GUSDEV] Incomplete generation of child relations from FK on PostgreSQL

[<an...@ne...>]

Hello all,
I've stumbled upon a bug in the PostgreSQL implementation of the Perl obj=
ect
layer: when generating Perl objects, most childRelations are missing even=
 if
the PostgreSQL database contains the relevant FK constraint.

The same bug shows up on two different PostgreSQL versions, namely 8.1.4 =
and
7.4.13.

The problem lies in file '$PROJECT_HOME/GUS/ObjRelP/lib/perl/PostgreSQL.p=
m':
the subroutine 'tableChildRelationsSql' returns incorrect (schema names a=
re
reversed) and incomplete (filtering by schema name discards relations to
external schemas) data.

I'm attaching a file 'query.pl' that shows the problem on child relations=
 for
table 'GUS::Model::SRes::Contact', and a modified version of PostgreSQL.p=
m with
a query that works correctly for me.

Here is the output with the original query:

TABLE GUS::Model::SRes::Contact
---- Child relations from $db->getTableChildRelations
GUS::Model::SRes::BibliographicReference, contact_id, contact_id
GUS::Model::SRes::Contact, contact_id, affiliation_id
------------

While this is the output with the modified SQL (incidentally, this very s=
ame
output should be what is obtained from a working installation on Oracle):

TABLE GUS::Model::SRes::Contact
---- Child relations from $db->getTableChildRelations
GUS::Model::Core::UserInfo, contact_id, contact_id
GUS::Model::DoTS::AASequenceEnzymeClass, contact_id, ec_assignment_contac=
t_id
GUS::Model::DoTS::Attribution, contact_id, contact_id
GUS::Model::DoTS::CloneSet, contact_id, contact_id
GUS::Model::DoTS::EST, contact_id, contact_id
GUS::Model::DoTS::NASequenceImp, contact_id, sequencing_center_contact_id
GUS::Model::RAD::Analysis, contact_id, operator_id
GUS::Model::RAD::ArrayDesign, contact_id, manufacturer_id
GUS::Model::RAD::Assay, contact_id, operator_id
GUS::Model::RAD::Quantification, contact_id, operator_id
GUS::Model::SRes::BibliographicReference, contact_id, contact_id
GUS::Model::SRes::Contact, contact_id, affiliation_id
GUS::Model::Study::BioMaterialImp, contact_id, bio_source_provider_id
GUS::Model::Study::Study, contact_id, contact_id
------------

Is there anyone using GUSDB on PostgreSQL who can confirm this issue and =
test
that my solution does not break anything else?

Thanks a lot in advance,

Antonio Galea



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This message was sent using IMP, the Internet Messaging Program.

[GUSDEV] Description of tables - documentation

[Ana C. <an...@ig...>]

Hello all! 

I need to know the description/definition of some terms that don't have in 
gus schema browser. 
Can you help me??? 
1- Table NASequence 
SEQUENCE_PIECE_ID 
2- Table Similarity 
BIT_SCORE_SUMMARY 
3- Table SimilaritySpan 
BIT_SCORE 
4- Table NALocation 
LOC_ORDER 
IS_EXCLUDED 
DB_NAME 
DB_IDENTIFIER 
LITERAL_SEQUENCE 
REMARK 
DEBUG_FIELD 
5- Table NAProtein/NAGene 
IS_VERIFIED 

I need this to put in my final dissertation of master's degree and i don't 
know biology very well, but I studied GUS more or less... 

Thanks in advance, 
Ana Carolina 

Re: [GUSDEV] path/env config files in gus

[Steve F. <sfi...@pc...>]

michael-

gus gets its bioperl from the standard perl location.   you install 
bioperl using cpan, and then it is available in the regular perl path.

steve

mro...@cs... wrote:
> Hello folks;
>
> We have Gus 3.5 installed and have been able to to load the taxon data,
> now while trying to use InsertSequenceFeatures.pl which uses BioPerl, we
> have the following problem:
>
> We have 2 different versions of Perl, and Bioperl is installed in a
> different computer, I have been looking for the config files that Gus uses
> to look for Bioperl.
>
> I found and modified:
>  $GUS_HOME/config/install.pro
>
> but it seems that there are other file(s) that need to be modified
>
> Does anybody know where they are?
>
>
> Cheers,
> Michael Robinson
> Bioinformatics Research Group (BioRG)
> Florida International University
> Miami FL 33199
>
>
>
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
> opinions on IT & business topics through brief surveys -- and earn cash
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> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>   

[GUSDEV] path/env config files in gus

[<mro...@cs...>]

Hello folks;

We have Gus 3.5 installed and have been able to to load the taxon data,
now while trying to use InsertSequenceFeatures.pl which uses BioPerl, we
have the following problem:

We have 2 different versions of Perl, and Bioperl is installed in a
different computer, I have been looking for the config files that Gus use=
s
to look for Bioperl.

I found and modified:
 $GUS_HOME/config/install.pro

but it seems that there are other file(s) that need to be modified

Does anybody know where they are?


Cheers,
Michael Robinson
Bioinformatics Research Group (BioRG)
Florida International University
Miami FL 33199

[GUSDEV] How to populate the GUS schema with external databases after installing.

[Roger U. <un...@sd...>]

Hi,

I have followed the installguide.pdf for GUS, and successfully  
completed all instructions in it ending with the following two commands:
	build GUS install -append -installDBSchema
	ga +meta --commit

The problem is that I am unable to locate instructions/examples for  
populating GUS with data from external databases.  If anyone can  
point me to some documentation on this, I would appreciate it.

Thanks,

Roger
--
Roger Unwin
un...@sd...

[GUSDEV] upgrading GUS & @INC

[marc j. <de...@ho...>]

Hello,

I'm trying to upgrade GUS to the latest release from 3.0.
I'm trying to use DumpSchema.pl and @INC is way off.
I modified the script to point to the correct library and
it's still off.  Where's the config file for the perl scripts
that would allow me to make one change.

Regards,

Marc

Re: [GUSDEV] Blast Similarities

[Mark S. H. <mh...@ug...>]

Hi Adhemar,

See comments inline...

On Jul 11, 2006, at 12:50 PM, Adhemar Zerlotini Neto wrote:

> I'm trying to upload some blast results following a manual created  
> by Pablo, from Jessica's Lab. at UGA.
>
> The problem is that the perl script  
> 'parseBlastFilesForSimilarity.pl' isn't working.
>
> Here is the error:
>

<extraneous error msg cut>

> Analyzing
> opening
> /home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/ 
> SJest.VS.SJcontigs.PARSED
> Can't locate object method "new" via package "Blast::BlastAnal"
> (perhaps you forgot to load "Blast::BlastAnal"?) at
> parseBlastFilesForSimilarity.pl line 81.
>
>

This looks like the same problem as before - the script is looking  
for 'Blast::BlastAnal ' but the correct package name is  
CBIL::Bio::Blast::BlastAnal.

> I would like to know how to fix this script or to download a new  
> version of the blast parse scripts.
>

We use the DJob framework for our blast execution and result parsing.  
https://cbil.upenn.edu/svn/gus/DJob/trunk/DistribJob/doc/DistribJob.html

Within the DJob project is a blastSimilarity script. Your  
parseBlastFilesForSimilarity.pl script appears to be pretty much the  
same as DJob's blastSimilarity except blastSimilarity also executes  
the blast command in addition to parsing the result. I don't know of  
any other supported blast parsing script.

The output of blastSimilarity can be loaded into GUS with  
GUS::Supported::Plugin::InsertBlastSimilarities. I believe that's the  
same for your parseBlastFilesForSimilarity.pl

DJob is well documented and a very useful system if you use a compute  
cluster or have several types  of analyses that you want to wrap in a  
pipeline. If you are running your blast on a single machine and just  
want to parse the results for loading into GUS then you will probably  
want to continue to use the parseBlastFilesForSimilarity script.

In summary, fix the package name in your script and continue to use  
that. Email Pablo or me directly if you continue to have problems  
with parseBlastFilesForSimilarity.

-Mark

[GUSDEV] Blast Similarities

[Adhemar Z. N. <ad...@cp...>]

I'm trying to upload some blast results following a manual created by
Pablo, from Jessica's Lab. at UGA. <br /><br />The problem is that the
perl script '<font size=3D"2"><span style=3D"font-family: courier
new,courier,monospace;">parseBlastFilesForSimilarity.pl'
</span></font>isn't working.<br /><br />Here is the error:<br /><br
/><font size=3D"2"><span style=3D"font-family: courier
new,courier,monospace;">perl parseBlastFilesForSimilarity.pl
--regex=3D'(\S+)'</span><br style=3D"font-family: courier
new,courier,monospace;" /><span style=3D"font-family: courier
new,courier,monospace;">--outputFile=3D/home/japonicum/JaponicumDB/PROJEC=
TS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED</span><br
style=3D"font-family: courier new,courier,monospace;" /><span
style=3D"font-family: courier
new,courier,monospace;">--dir=3D/home/japonicum/JaponicumDB/PROJECTS_INFO=
/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.RESULTS</span><br
style=3D"font-family: courier new,courier,monospace;" /><span
style=3D"font-family: courier new,courier,monospace;">Opening</span><br
style=3D"font-family: courier new,courier,monospace;" /><span
style=3D"font-family: courier
new,courier,monospace;">/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/S=
Jest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED</span><br
style=3D"font-family: courier new,courier,monospace;" /><span
style=3D"font-family: courier
new,courier,monospace;">/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/S=
Jest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED</span><br
style=3D"font-family: courier new,courier,monospace;" /><span
style=3D"font-family: courier new,courier,monospace;">is open</span><br
style=3D"font-family: courier new,courier,monospace;" /><span
style=3D"font-family: courier new,courier,monospace;">Cutoff
parameters:</span><br style=3D"font-family: courier new,courier,monospace=
;"
/><span style=3D"font-family: courier new,courier,monospace;">=A0P value:
1e-05</span><br style=3D"font-family: courier new,courier,monospace;"
/><span style=3D"font-family: courier new,courier,monospace;">=A0Length:
10</span><br style=3D"font-family: courier new,courier,monospace;" /><spa=
n
style=3D"font-family: courier new,courier,monospace;">=A0Percent Identity=
:
20</span><br style=3D"font-family: courier new,courier,monospace;" /><br
style=3D"font-family: courier new,courier,monospace;" /><br
style=3D"font-family: courier new,courier,monospace;" /><span
style=3D"font-family: courier new,courier,monospace;">Analyzing</span><br
style=3D"font-family: courier new,courier,monospace;" /><span
style=3D"font-family: courier new,courier,monospace;">opening</span><br
style=3D"font-family: courier new,courier,monospace;" /><span
style=3D"font-family: courier
new,courier,monospace;">/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/S=
Jest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED</span><br
style=3D"font-family: courier new,courier,monospace;" /><span
style=3D"font-family: courier new,courier,monospace;">Can't locate object
method &quot;new&quot; via package &quot;Blast::BlastAnal&quot;</span><br
style=3D"font-family: courier new,courier,monospace;" /><span
style=3D"font-family: courier new,courier,monospace;">(perhaps you forgot=
 to
load &quot;Blast::BlastAnal&quot;?) at</span><br style=3D"font-family:
courier new,courier,monospace;" /><span style=3D"font-family: courier
new,courier,monospace;">parseBlastFilesForSimilarity.pl line
81.</span></font><br />=A0<br />=A0<br />I would like to know how to fix =
this
script or to download a new version of the blast parse scripts.<br /><br
/>Thanks,<br /><br />Ad.<br /><br />

[GUSDEV] Blast Similarities

[Adhemar Z. N. <ad...@cp...>]

I'm trying to upload some blast results following a manual created by
Pablo, from Jessica's Lab. at UGA.<br /><br />The problem is that the per=
l
script 'parseBlastFilesForSimilarity.pl' isn't working.<br /><br />Here i=
s
the error:<br /><br /><font size=3D"2" style=3D"font-family: courier
new,courier,monospace;">perl parseBlastFilesForSimilarity.pl
--regex=3D'(\S+)'<br
/>--outputFile=3D/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS=
.SJcontigs/SJest.VS.SJcontigs.PARSED<br
/>--dir=3D/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcont=
igs/SJest.VS.SJcontigs.RESULTS<br
/>Opening<br
/>/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJes=
t.VS.SJcontigs.PARSED<br
/>/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJes=
t.VS.SJcontigs.PARSED<br
/>is open<br />Cutoff parameters:<br />=A0P value: 1e-05<br />=A0Length: =
10<br
/>=A0Percent Identity: 20<br /><br /><br />Analyzing<br />opening<br
/>/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJes=
t.VS.SJcontigs.PARSED<br
/>Can't locate object method &quot;new&quot; via package
&quot;Blast::BlastAnal&quot;<br />(perhaps you forgot to load
&quot;Blast::BlastAnal&quot;?) at<br />parseBlastFilesForSimilarity.pl
line 81.</font><br />=A0<br />=A0<br />I would like to know how to fix th=
is
script or to download a new version of the blast parse scripts.<br /><br
/>Thanks,<br /><br />Ad.<br /><br />

[GUSDEV] [ Re: Blast Similarities]

[Adhemar Z. N. <ad...@cp...>]

<ad...@cp...><gus...@li...>Now it's
working. I changed all 'Blast::BlastAnal' entries in the perl script file
to 'CBIL::Bio::Blast::BlastAnal' and it worked. <br /><br />As you and
Steve told it isn't a supported script, I wonder if you could publish the
supported scripts and documentation for uploading blast results. <br /><b=
r
/>Thanks,<br />Ad.<br /><br /><br /> <br /><br /><br />Adhemar Zerlotini
Neto<br />Centro de Pesquisas Ren=E9 Rachou - FIOCRUZ<br />Av. Augusto de
Lima 1715<br />BH MG 30190-002, Brazil<br />Phone:
+55-31-3349-7785</gus...@li...></ad...@cp...o=
cruz.br>

Re: [GUSDEV] Out of Memory while loading Taxonomy data

[<ju...@cs...>]

pi...@pc... (Debbie) writes:
>
> LoadTaxonomy was written to update taxon_id in child tables prior to deleting
> the row in taxon_id so I suspect that something else is happening, for example
> a group_write or group_id issue.

No, the problem is as I describe.
Yes, obviously the intent behind LoadTaxon would have been to update
taxon_id in all child tables first, but this is not happening.
LoadTaxon is broken.


> >> GUS::Model::SRes::Taxon=3DHASH(0x9ee9e54)
> >> DBD::Oracle::db do failed: ORA-02292: integrity constraint
> >> (DOTS.NASEQUENCEIMP_FK02) violated - child record found (DBD
> >> ERROR:OCIStmtExecute)
> >>  [for Statement "DELETE FROM SRes.Taxon WHERE  taxon_id = 525455
> >> "] at /home/oragus35/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
> >> line 119, <MERGED> line 5476.
> >> [...]

Re: [GUSDEV] Out of Memory while loading Taxonomy data

[<pi...@pc...>]

LoadTaxonomy was written to update taxon_id in child tables prior to deleting
the row in taxon_id so I suspect that something else is happening, for example
a group_write or group_id issue.

Debbie

Quoting Josef Jurek <ju...@cs...>:

>
> "Kumar, Sanjeev" <San...@ng...> writes:
>>
>> But I am getting a new type of error message, provided below. Can some
>> one pl. help me in understanding/resolving the error message.
>>
>>
>> GUS::Model::SRes::Taxon=3DHASH(0xa166cf8) merged with Taxon_id =3D
>> GUS::Model::SRes::Taxon=3DHASH(0x9ee9e54)
>> DBD::Oracle::db do failed: ORA-02292: integrity constraint
>> (DOTS.NASEQUENCEIMP_FK02) violated - child record found (DBD 
>> ERROR:OCIStmtExecute)
>>  [for Statement "DELETE FROM
>> SRes.Taxon WHERE  taxon_id =3D 525455
>> "] at /home/oragus35/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
>> line 119, <MERGED> line 5476.
>> [...]
>
> I ran into this very same error as well.  What is happening
> is that LoadTaxon is attempting to delete obsolete
> taxonomy entries _however_ some of these taxonomy
> entries are still referenced by the TAXON_ID field
> of DoTS.NASequence.
>
> What LoadTaxon _should_ _do_ is update all places
> in DoTS.NASequence/DoTS.AASequence (and possibly
> other tables) so that obsolete taxonomy entries
> are replace in the tables that reference
> them _before_ LoadTaxon tries to delete them
> from SRes.Taxon.
>
> My jury-rig (and I do mean jury-rig) was
> to run a perl script on merged.dmp to
> convert each data line to a SQL line which
> might look like:
>
>  update DoTS.ExternalAASequence set taxon_id = 255892 where taxon_id 
> = 256194;
>
> thus, updating the taxon_id fields.
>
> When it comes to updating Taxonomy information
> LoadTaxon does not appear to be very robust.
>
> Josef
>
>
>
> Josef Jurek, Ph.D.
>
> Daphne Preuss Laboratory
> Molecular Genetics and Cell Biology
> The University of Chicago
> ju...@cs...
>
> voice: (773) 702-9559
> fax:   (773) 702-6648
>
>
>
>
>
>
>
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>

Re: [GUSDEV] Out of Memory while loading Taxonomy data

[<jl...@vb...>]

What I did to update taxonomy is to use SQL commnds. Assume you only have
taxon_id on DoTS.Sequence table.
1. Backup your old taxon_id
SQL>CREATE TABLE DoTS.NASequenceTaxonID AS
select a.na_sequence_id, a.taxon_id, b.ncbi_tax_id from dots.nasequence a,
sres.taxon b where a.taxon_id=b.taxon_id;

2. Delete taxon_id on DoTS.Sequence table
SQL>update dots.nasequence set taxon_id = null;

3. Delete taxonomy data
SQL>delete from sres.taxonname;
SQL>delete from sres.taxon;

4.Run plugin to load new taxonomy data

5.Restore taxon_id on DoTS.Sequence table
SQL>update dots.nasequence s set taxon_id=(select b.taxon_id from
dots.nasequencetaxonid a, sres.taxon b
where a.ncbi_tax_id=b.ncbi_tax_id and a.na_sequence_id=s.na_sequence_id);


On Wed, July 12, 2006 1:31 pm, Josef Jurek wrote:
>

> "Kumar, Sanjeev" <San...@ng...> writes:
>
>>
>> But I am getting a new type of error message, provided below. Can some
>> one pl. help me in understanding/resolving the error message.
>>
>>
>> GUS::Model::SRes::Taxon=3DHASH(0xa166cf8) merged with Taxon_id =3D
>> GUS::Model::SRes::Taxon=3DHASH(0x9ee9e54)
>> DBD::Oracle::db do failed: ORA-02292: integrity constraint
>> (DOTS.NASEQUENCEIMP_FK02) violated - child record found (DBD
>> ERROR:OCIStmtExecute)
>> [for Statement "DELETE FROM
>> SRes.Taxon WHERE  taxon_id =3D 525455
>> "] at /home/oragus35/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
>> line 119, <MERGED> line 5476. [...]
>>
>
> I ran into this very same error as well.  What is happening
> is that LoadTaxon is attempting to delete obsolete taxonomy entries
> _however_ some of these taxonomy
> entries are still referenced by the TAXON_ID field of DoTS.NASequence.
>
> What LoadTaxon _should_ _do_ is update all places
> in DoTS.NASequence/DoTS.AASequence (and possibly other tables) so that
> obsolete taxonomy entries are replace in the tables that reference them
> _before_ LoadTaxon tries to delete them
> from SRes.Taxon.
>
> My jury-rig (and I do mean jury-rig) was
> to run a perl script on merged.dmp to convert each data line to a SQL line
> which might look like:
>
> update DoTS.ExternalAASequence set taxon_id = 255892 where taxon_id =
> 256194;
>
>
> thus, updating the taxon_id fields.
>
> When it comes to updating Taxonomy information
> LoadTaxon does not appear to be very robust.
>
>
> Josef
>
>
>
>
> Josef Jurek, Ph.D.
>
>
> Daphne Preuss Laboratory
> Molecular Genetics and Cell Biology
> The University of Chicago
> ju...@cs...
>
> voice: (773) 702-9559
> fax:   (773) 702-6648
>
>
>
>
>
>
>
>
>
> -------------------------------------------------------------------------
>  Using Tomcat but need to do more? Need to support web services,
> security? Get stuff done quickly with pre-integrated technology to make
> your job easier Download IBM WebSphere Application Server v.1.0.1 based on
> Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
>

Re: [GUSDEV] Blast Similarities

[Adhemar Z. N. <ad...@cp...>]

Now it's working. I changed all 'Blast::BlastAnal' in the perl script file
to 'CBIL::Bio::Blast::BlastAnal' and it worked. <br /><br />As you and
Steve told it isn't a supported script, I wonder if you could publish the
supported scripts and documentation for uploading blast results. <br /><br
/>Thanks,<br />Ad.<br /><br /><br />

Re: [GUSDEV] Out of Memory while loading Taxonomy data

[<ju...@cs...>]

"Kumar, Sanjeev" <San...@ng...> writes:
>
> But I am getting a new type of error message, provided below. Can some
> one pl. help me in understanding/resolving the error message.
>
>
> GUS::Model::SRes::Taxon=3DHASH(0xa166cf8) merged with Taxon_id =3D
> GUS::Model::SRes::Taxon=3DHASH(0x9ee9e54)
> DBD::Oracle::db do failed: ORA-02292: integrity constraint
> (DOTS.NASEQUENCEIMP_FK02) violated - child record found (DBD ERROR:OCIStmtExecute)
>  [for Statement "DELETE FROM
> SRes.Taxon WHERE  taxon_id =3D 525455
> "] at /home/oragus35/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm
> line 119, <MERGED> line 5476.
> [...]

I ran into this very same error as well.  What is happening
is that LoadTaxon is attempting to delete obsolete
taxonomy entries _however_ some of these taxonomy
entries are still referenced by the TAXON_ID field
of DoTS.NASequence.

What LoadTaxon _should_ _do_ is update all places
in DoTS.NASequence/DoTS.AASequence (and possibly
other tables) so that obsolete taxonomy entries
are replace in the tables that reference
them _before_ LoadTaxon tries to delete them
from SRes.Taxon.

My jury-rig (and I do mean jury-rig) was
to run a perl script on merged.dmp to
convert each data line to a SQL line which
might look like:

  update DoTS.ExternalAASequence set taxon_id = 255892 where taxon_id = 256194;

thus, updating the taxon_id fields.

When it comes to updating Taxonomy information
LoadTaxon does not appear to be very robust.

Josef



Josef Jurek, Ph.D.

Daphne Preuss Laboratory
Molecular Genetics and Cell Biology
The University of Chicago
ju...@cs...

voice: (773) 702-9559
fax:   (773) 702-6648

Re: [GUSDEV] Reply for LoadTaxonomy issue

[<pi...@pc...>]

Sorry, I read two messages and replied to the wrong one. Obviously this reply
concerns the LoadTaxonomy plugin problem.




Quoting pi...@pc...:

> One possibility:
>
> You might not be in the right group or group write is not set properly on the
> child table. If true, the plugin is not able to update the child row's
> taxon_id
> and therefore deleting that taxon row would violate a foreign key constraint.
> Check the core.groupinfo for which group you're in and the group_write
> field in
> the child table.
>
> Debbie
>
>
>
>
> Quoting Pablo Mendes <pa...@ug...>:
>
>>
>> Hi Adhemar,
>> it seems you need the BlastAnal.pm package
>>
>>> Can't locate object method "new" via package "Blast::BlastAnal"
>>> (perhaps you forgot to
>>> load "Blast::BlastAnal"?) at
>>
>> It is available in a CBIL tar:
>> http://www.cbil.upenn.edu/downloads/CBIL/releases/
>>
>> CBIL/Bio/lib/perl/Blast/BlastAnal.pm
>>
>> You might want to change/add a "use lib" to
>> 'parseBlastFilesForSimilarity.pl' or to add the CBIL to your
>> "classpath", changing the $PERL5LIB variable.
>> (http://www.perl.com/doc/manual/html/pod/perlrun.html)
>>
>>
>> Good luck,
>> Pablo
>>  ----- Original Message -----
>>  From: Adhemar Zerlotini Neto
>>  To: gus...@li...
>>  Sent: Wednesday, July 12, 2006 11:31 AM
>>  Subject: [GUSDEV] Blast Similarities
>>
>>
>>  I'm trying to upload some blast results following a manual created
>> by Pablo, who works at Jessica's Lab. at UGA.
>>
>>  The problem is that the perl script
>> 'parseBlastFilesForSimilarity.pl' isn't working.
>>
>>  Here is the error:
>>
>>  perl parseBlastFilesForSimilarity.pl --regex='(\S+)'
>>
>> --outputFile=/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED 
>> --dir=/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.RESULTS
>> Opening
>>
>> /home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED /home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED 
>> is
>> open
>>  Cutoff parameters:
>>  P value: 1e-05
>>  Length: 10
>>  Percent Identity: 20
>>
>>
>>  Analyzing
>>  opening
>>
>> /home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED Can't locate object method "new" via package "Blast::BlastAnal" (perhaps you forgot to load 
>> "Blast::BlastAnal"?)
>> at
>>  parseBlastFilesForSimilarity.pl line 81.
>>
>>
>>  I would like to know how to fix this script or to download a new
>> version of the blast parse scripts.
>>
>>  Thanks,
>>
>>  Ad.
>>
>>
>>
>>
>>
>> ------------------------------------------------------------------------------
>>
>>
>>
>>  -------------------------------------------------------------------------
>>  Using Tomcat but need to do more? Need to support web services, security?
>>  Get stuff done quickly with pre-integrated technology to make your
>> job easier
>>  Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
>>  http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
>>
>>
>>
>> ------------------------------------------------------------------------------
>>
>>
>>  _______________________________________________
>>  Gusdev-gusdev mailing list
>>  Gus...@li...
>>  https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>
>
>
>
>
>
> -------------------------------------------------------------------------
> Using Tomcat but need to do more? Need to support web services, security?
> Get stuff done quickly with pre-integrated technology to make your job easier
> Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>