SF.net SVN: gmod:[22222] schema/trunk/chado/MANIFEST

[scottcain]

Revision: 22222
          http://gmod.svn.sourceforge.net/gmod/?rev=22222&view=rev
Author:   scottcain
Date:     2009-11-04 14:20:24 +0000 (Wed, 04 Nov 2009)

Log Message:
-----------
lots of updates to manifest

Modified Paths:
--------------
    schema/trunk/chado/MANIFEST

Modified: schema/trunk/chado/MANIFEST
===================================================================
--- schema/trunk/chado/MANIFEST 2009-11-03 23:32:32 UTC (rev 22221)
+++ schema/trunk/chado/MANIFEST 2009-11-04 14:20:24 UTC (rev 22222)
@@ -4,7 +4,11 @@
 bin/chado-fix-flybase-instance.pl
 bin/config.PLS
 bin/create-bridge-sql.pl
+bin/create-so-bridge.pl
+bin/cxgn/gmod_load_cvterms.pl
 bin/cxgn/load_cvterms.pl
+bin/cxgn/load_ncbi_taxonomy.pl
+bin/cxgn/load_taxonomy_cvterms.pl
 bin/dbi.tt2
 bin/ddltrans
 bin/gencode2sql.pl
@@ -47,6 +51,8 @@
 chado-xml/xsl/chado-remove-feature-nesting.xsl
 chado-xml/xsl/README
 Changes
+Changes.GMOD
+Changes.sql
 chaos-xml/bin/cx-chadoxml2chaos.pl
 chaos-xml/bin/cx-chaos-report.pl
 chaos-xml/bin/cx-download-enscore.pl
@@ -77,6 +83,7 @@
 chaos-xml/xsl/cx-chaos-to-gff3.xsl
 chaos-xml/xsl/README
 Class-DBI-Pg-0.06-multiple-schemata.patch
+conf/bulkfiles/anogam.xml
 conf/bulkfiles/blastfiles.xml
 conf/bulkfiles/bulkfiles_template.xml
 conf/bulkfiles/chadofeatconv.xml
@@ -88,6 +95,7 @@
 conf/bulkfiles/dpsebulk-p4.xml
 conf/bulkfiles/dpsebulk-p5.xml
 conf/bulkfiles/dpsebulk-r2.xml
+conf/bulkfiles/drosmelgb.xml
 conf/bulkfiles/fastawriter.xml
 conf/bulkfiles/fbbulk-hetr3.xml
 conf/bulkfiles/fbbulk-r3.xml
@@ -100,6 +108,7 @@
 conf/bulkfiles/filesets.xml
 conf/bulkfiles/gbrowseconf.xml
 conf/bulkfiles/gbrowseconf_fb.xml
+conf/bulkfiles/genbanksubmit.xml
 conf/bulkfiles/genomeweb.xml
 conf/bulkfiles/organisms.xml
 conf/bulkfiles/sgdbulk.xml
@@ -107,6 +116,8 @@
 conf/bulkfiles/sgdfeatconf.xml
 conf/bulkfiles/site_defaults.xml
 conf/bulkfiles/site_eugenes_defaults.xml
+conf/bulkfiles/spbase.xml
+conf/bulkfiles/spbasefeatconf.xml
 conf/bulkfiles/tablewriter.xml
 conf/bulkfiles/toacode.xml
 conf/bulkfiles/tognomap.xml
@@ -133,14 +144,15 @@
 install_util/install.pm
 install_util/log4perl.conf.PLS
 install_util/src_install.PLS
-lib/Bio/FeatureIO/chado.pm
-lib/Bio/FeatureIO/chadobulk.pm
+lib/Bio/Chado/Builder.pm
+lib/Bio/Chado/Config.pm
 lib/Bio/GMOD/Bulkfiles.pm
 lib/Bio/GMOD/Bulkfiles/AcodeWriter.pm
 lib/Bio/GMOD/Bulkfiles/BlastWriter.pm
 lib/Bio/GMOD/Bulkfiles/BulkWriter.pm
 lib/Bio/GMOD/Bulkfiles/FastaWriter.pm
 lib/Bio/GMOD/Bulkfiles/FeatureWriter.pm
+lib/Bio/GMOD/Bulkfiles/GenbankSubmitWriter.pm
 lib/Bio/GMOD/Bulkfiles/GnomapWriter.pm
 lib/Bio/GMOD/Bulkfiles/MyLargePrimarySeq.pm
 lib/Bio/GMOD/Bulkfiles/MySplitLocation.pm
@@ -150,65 +162,15 @@
 lib/Bio/GMOD/Config2.pm
 lib/Bio/GMOD/DB/Adapter.pm
 lib/Bio/GMOD/DB/Adapter/FeatureIterator.pm
+lib/Bio/GMOD/DB/Adapter/Wormbase.pm
 lib/Bio/GMOD/DB/Config.pm
 lib/Bio/GMOD/DB/Tools/ETA.pm
 lib/Bio/GMOD/Load.pm
 lib/Bio/GMOD/Load/GFF.pm
 lib/Bio/GMOD/SeqUtils.pm
-lib/Bio/Chado/Builder.pm
-lib/Bio/Chado/Config.pm
-lib/CXGN/Chado/CV.pm
-lib/CXGN/Chado/Cvterm.pm
-lib/CXGN/Chado/Db.pm
-lib/CXGN/Chado/Dbxref.pm
-lib/CXGN/Chado/Feature.pm
-lib/CXGN/Chado/FeatureLoc.pm
-lib/CXGN/Chado/Main.pm
-lib/CXGN/Chado/Ontology.pm
-lib/CXGN/Chado/Organism.pm
-lib/CXGN/Chado/Phenotype.pm
-lib/CXGN/Chado/Pubauthor.pm
-lib/CXGN/Chado/Publication.pm
-lib/CXGN/Chado/Relationship.pm
-lib/CXGN/Class/Exporter.pm
-lib/CXGN/Configuration.pm
-lib/CXGN/DB/Connection.pm
-lib/CXGN/DB/Ima.pm
-lib/CXGN/DB/InsertDBH.pm
-lib/CXGN/DB/Loader.pm
-lib/CXGN/DB/Object.pm
-lib/CXGN/LICENSE
-lib/CXGN/Tools/AnnotationConsensus.pm
-lib/CXGN/Tools/Chado.pm
-lib/CXGN/Tools/Class.pm
-lib/CXGN/Tools/Cluster.pm
-lib/CXGN/Tools/Entrez.pm
-lib/CXGN/Tools/ExternalFile.pm
-lib/CXGN/Tools/FeatureFetch.pm
-lib/CXGN/Tools/File.pm
-lib/CXGN/Tools/Gene.pm
-lib/CXGN/Tools/Identifiers.pm
-lib/CXGN/Tools/List.pm
-lib/CXGN/Tools/Organism.pm
-lib/CXGN/Tools/Param.pm
-lib/CXGN/Tools/Parse.pm
-lib/CXGN/Tools/PgCatalog.pm
-lib/CXGN/Tools/Pubmed.pm
-lib/CXGN/Tools/RestrictionEnzyme.pm
-lib/CXGN/Tools/Run.pm
-lib/CXGN/Tools/RunTime.pm
-lib/CXGN/Tools/Script.pm
-lib/CXGN/Tools/Sequence.pm
-lib/CXGN/Tools/Terminal.pm
-lib/CXGN/Tools/Text.pm
-lib/CXGN/Tools/WebImageCache.pm
-lib/CXGN/Tools/Wget.pm
-lib/CXGN/VHost.pm
 LICENSE
 load/bin/bulk_load_gff3.PLS
-load/bin/load_affymetrix.pl
-load/bin/load_affyxls.pl
-load/bin/load_taxonomy.pl
+load/bin/load_gff3.PLS
 load/Build.PL
 load/etc/chap.obo
 load/etc/extra.sql
@@ -228,6 +190,7 @@
 modules/audit/make_audit_ddl
 modules/bin/makedep.pl
 modules/bin/mk.pl
+modules/cell_line/cell_line.sql
 modules/companalysis/companalysis.html
 modules/companalysis/companalysis.sql
 modules/companalysis/functions/companalysis-loading.plpgsql
@@ -312,6 +275,7 @@
 modules/sequence/bridges/bin/create-sofa-bridge.pl
 modules/sequence/bridges/chaos-bridge.sql.xml
 modules/sequence/bridges/gadfly-bridge.sql.xml
+modules/sequence/bridges/so-bridge.sql
 modules/sequence/bridges/sofa-bridge.sql
 modules/sequence/functions/create_soi.plpgsql
 modules/sequence/functions/delete-trigger.plpgsql
@@ -342,6 +306,7 @@
 modules/sequence/sequence.sql
 modules/sequence/sequence_opt.xml
 modules/sequence/sequence_views.sql
+modules/sequence/views/exon-views.sql
 modules/sequence/views/implicit-feature-views.sql
 modules/sequence/views/range-views.sql
 modules/sequence/views/sequence-cv-views.sql


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