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Index of /KBaseCDMI

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File Rev. Age Author Last log entry
 Parent Directory        
Bio/        
Iris/        
anno_scripts/        
anno_service_scripts/        
entity-api/        
er_scripts/        
iscripts/        
scripts/        
tree_scripts/        
AskKB.spec  1.2  5 years  disz  Added Save
CDM6ContigCheck.pl  1.1  3 years  parrello  New script for finding bad contigs.
CDMI-API.spec  1.40  3 years  olson  Bugfix for aliases_to_fids. Add source_ids_to_fids.
CDMI-EntityAPI.spec  1.23  2 years  olson  Genome annotation checkpoint.
CDMI.psgi  1.3  4 years  olson  Big update for new doc reformatting and --help support.
CDMICheck.pl  1.2  3 years  parrello  Loader changes, new fixup utilities.
CDMICheck2.pl  1.1  3 years  parrello  Loader changes, new fixup utilities.
CDMICheckDB.pl  1.1  3 years  parrello  Incremental loader updates.
CDMICheckFunctions.pl  1.2  2 years  parrello  New rast-based loader. Update to DBD.
CDMIClean.pl  1.2  3 years  parrello  New utilities for fixing database errors.
CDMICreate.pl  1.5  2 years  parrello  New rast-based loader. Update to DBD.
CDMIDeleteCheck.pl  1.1  3 years  parrello  Loader changes, new fixup utilities.
CDMIDeleteGenome.pl  1.4  3 years  parrello  Fixed a loader bug relating to subsystems. Added and updated many scripts relati...
CDMIDupFix.pl  1.4  3 years  parrello  Fixed a loader bug relating to subsystems. Added and updated many scripts relati...
CDMIEntities.pl  1.1  4 years  parrello  New script to list all the entities in a CDMI.
CDMIFillProteins.pl  1.1  3 years  parrello  Loader changes, new fixup utilities.
CDMIFindRedundantGenomes.pl  1.1  4 years  parrello  New script to find genomes for deletion.
CDMIFix.pl  1.11  3 years  parrello  Loader changes, new fixup utilities.
CDMIFix2.pl  1.3  3 years  parrello  Fixed a loader bug relating to subsystems. Added and updated many scripts relati...
CDMIFix3.pl  1.1  3 years  parrello  Loader changes, new fixup utilities.
CDMIFixBadGenomes.pl  1.2  3 years  parrello  Fixed a loader bug relating to subsystems. Added and updated many scripts relati...
CDMIFixBadLocations.pl  1.1  3 years  parrello  Fixed a loader bug relating to subsystems. Added and updated many scripts relati...
CDMIFixEntities.pl  1.2  3 years  parrello  Incremental loader updates.
CDMIFixFile.pl  1.1  3 years  parrello  Incremental loader updates.
CDMIFixFunctions.pl  1.2  3 years  parrello  Loader changes, new fixup utilities.
CDMIFixLocations.pl  1.2  3 years  parrello  Fixed a loader bug relating to subsystems. Added and updated many scripts relati...
CDMIFixPlantFile.pl  1.1  5 years  parrello  Model loader update
CDMIFixProteins.pl  1.1  3 years  parrello  CDMI and Sprout load fixes. Locations fixes.
CDMIFixRels.pl  1.2  3 years  parrello  Loader changes, new fixup utilities.
CDMIFlip.pl  1.1  4 years  parrello  New script for fixing an improperly-loaded relationship.
CDMIGenomeAnalysis.pl  1.1  4 years  parrello  Latest CDMI fixes
CDMIIDServerTest.pl  1.1  5 years  parrello  Model loader update
CDMILoadAlignments.pl  1.7  5 years  fangfang  add alignment_by_id and tree_by_id
CDMILoadAnnotations.pl  1.5  3 years  parrello  Incremental loader updates.
CDMILoadAssertions.pl  1.3  5 years  parrello  Switch to kbase_sapling_v1, POD documentation improvements, loader fixes.
CDMILoadBiochemistry.pl  1.2  3 years  parrello  Incremental loader updates.
CDMILoadBiochemistry_new.pl  1.1  3 years  parrello  Incremental loader updates.
CDMILoadCheck.pl  1.3  3 years  parrello  Fixed a loader bug relating to subsystems. Added and updated many scripts relati...
CDMILoadCodonUsage.pl  1.2  5 years  fangfang  Fix error in subtype column number
CDMILoadCoupling.pl  1.7  5 years  parrello  Switch to kbase_sapling_v1, POD documentation improvements, loader fixes.
CDMILoadExpression.pl  1.9  3 years  parrello  Incremental loader updates.
CDMILoadFIGfams.pl  1.6  5 years  parrello  Switch to kbase_sapling_v1, POD documentation improvements, loader fixes.
CDMILoadFamilies.pl  1.4  3 years  parrello  Incremental loader updates.
CDMILoadFromRast.pl  1.1  2 years  parrello  New rast-based loader. Update to DBD.
CDMILoadGenome.pl  1.20  3 years  parrello  Loader changes, new fixup utilities.
CDMILoadGenomeSets.pl  1.6  3 years  parrello  Incremental loader updates.
CDMILoadModels.pl  1.16  4 years  parrello  Fixed the column order on IsModeledBy.
CDMILoadPhenotypes.pl  1.1  5 years  parrello  Model loader update
CDMILoadProteins.pl  1.2  5 years  parrello  Switch to kbase_sapling_v1, POD documentation improvements, loader fixes.
CDMILoadPublications.pl  1.5  5 years  parrello  Switch to kbase_sapling_v1, POD documentation improvements, loader fixes.
CDMILoadRegPrecise.pl  1.5  4 years  parrello  Latest CDMI fixes
CDMILoadSubsystem.pl  1.13  3 years  parrello  Incremental loader updates.
CDMILoadTaxonomies.pl  1.7  3 years  parrello  Incremental loader updates.
CDMILoadVariations.pl  1.3  4 years  parrello  Added an option to keep the temporary files for debugging.
CDMIOrphanKiller.pl  1.2  5 years  parrello  Switch to kbase_sapling_v1, POD documentation improvements, loader fixes.
CDMIShortCheck.pl  1.1  3 years  parrello  Incremental loader updates.
CDMIStoreDBD.pl  1.2  5 years  parrello  Switch to kbase_sapling_v1, POD documentation improvements, loader fixes.
CDMISurvey.pl  1.1  4 years  parrello  Latest CDMI fixes
CDMITaxonomyFix.pl  1.2  3 years  parrello  Fixed a loader bug relating to subsystems. Added and updated many scripts relati...
CDMITaxonomyGenomes.pl  1.1  3 years  parrello  Fixed a loader bug relating to subsystems. Added and updated many scripts relati...
CDMITest.pl  1.11  3 years  parrello  Loader changes, new fixup utilities.
CDMIUnTar.pl  1.1  3 years  parrello  Fixed a loader bug relating to subsystems. Added and updated many scripts relati...
CDMIUpdateFunctions.pl  1.1  3 years  parrello  Incremental loader updates.
CDMIVerifyGenomes.pl  1.1  5 years  parrello  Model loader update
CdmiToSeedGenome.pl  1.2  5 years  parrello  Update prior to transferring to backup machine.
FastaFixup.pl  1.1  3 years  parrello  New utilities for fixing database errors.
GenomeAnnotation.js  1.5  2 years  olson  Genome annotation checkpoint.
GenomeAnnotation.psgi  1.3  2 years  olson  Genome annotation checkpoint.
GenomeAnnotation.py  1.5  2 years  olson  Genome annotation checkpoint.
GenomeAnnotation.spec  1.33  3 months  olson  Checkpoint / merge with git
IDServer-API.spec  1.2  5 years  olson  Updates to genome loader to use the ID server.
IDServerAPIClient.pm  1.2  5 years  olson  Reorganization of KBaseCDMI to use the new Bio::KBase namespace.
KBIDUtils.pm  1.1  5 years  parrello  KBase reorg part 4
KSaplingDBD.xml  1.40  2 years  parrello  New rast-based loader. Update to DBD.
KbaseFixup.pl  1.2  5 years  parrello  fids_to_literature fix, new loaders.
KbaseServerTest.pl  1.7  5 years  parrello  Directory restructuring fixes.
KmerEval.psgi  1.2  2 years  olson  Genome annotation checkpoint.
KmerEval.spec  1.1  4 years  disz  New Kmer modules
Makefile  1.14  2 years  olson  Genome annotation checkpoint.
MolToCdmiLoadFormat.pl  1.4  5 years  parrello  Converted to new source-aware ID system.
PlantsToCdmiLoadFormat.pl  1.4  5 years  parrello  Converted to new source-aware ID system.
README  1.1.1.1  5 years  olson  initial commit.
RelationLoader.pm  1.2  4 years  olson  Make relation tables world readable before loading.
SeedToCdmiLoadFormat.pl  1.8  3 years  parrello  Loader changes, new fixup utilities.
ValidCommands.pm.tt  1.1  5 years  olson  The template for ValidCommands.pm used by gen-valid-command.
Variations.pm  1.1  5 years  parrello  Protein family loader updates, other fixes.
build_cdmi_scripts  1.1  5 years  olson  write CDMI scripts from the spec file to a tmpdir
gen-valid-commands.pl  1.3  5 years  fangfang  add tree_scripts category
gen_cdmi_index.pl  1.2  5 years  parrello  Directory restructuring fixes.
gen_cdmi_sphinx_conf.pl  1.2  5 years  parrello  Loader fixes relating to index creation.
generate_script_skeleton  1.1  5 years  olson  Script to generate command-line script skeleton for a typespec function.
get.pl  1.1  4 years  parrello  Latest CDMI fixes
gitpub_genome_annotation  1.2  2 years  olson  Genome annotation checkpoint.
gitpub_invocation  1.1  4 years  olson  git publishing script
link_to_nowhere.pl  1.1  2 years  parrello  New rast-based loader. Update to DBD.
pipeline.yp  1.4  5 years  olson  Add valid_commands to invocation service. Add get_abundance_profile from Andreas...
recompile_genome_annotation  1.3  2 years  olson  Genome annotation checkpoint.
recompile_kmer_eval  1.2  4 years  olson  use differnet compiler
recompile_typespec  1.6  2 years  olson  Genome annotation checkpoint.
rewrite-comments.pl  1.1  4 years  olson  script to update comment format
sphinx.conf.tt  1.2  5 years  olson  sphinx fixes
update-library-documentation  1.2  2 years  olson  Genome annotation checkpoint.
write_doc_pages.pl  1.1  4 years  olson  The rest of the document processing scripts.
write_script_doc_pages.pl  1.1  4 years  olson  The rest of the document processing scripts.

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