[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