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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