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Get Started

  • Quick start guide
  • Description

Files

  • database.ini
  • setup.ini
  • default.ini
  • operophtera_brumata_core_32_85_1.ini

Importing data

  • Requirements
  • Running the EasyImport container
  • `-s` Create database and load sequence data
  • `-p` Prepare the gff file for import
  • `-g` Import gff from prepared file
  • `-v` Verify import
  • `-b -r -c` Import additional annotations
  • `-e -j -f` Export files
  • `-i` Generate search index
  • `-u` Update meta table

Additional documentation

  • Match and replace
  • Processing exceptions
  • Referencing gff attributes
  • Repairing gff

Configuration Options (Hosting)

  • [DATABASE]
  • [ENSEMBL_USER]
  • [REPOSITORIES]
  • [WEBSITE]
  • [DATA_SOURCE]

Configuration Options (Database)

  • [DATA_SOURCE]
  • [DATABASE]
  • [WEBSITE]

Configuration Options (Core Import)

  • [DATABASE_CORE]
  • [DATABASE_SEARCH]
  • [DATABASE_TAXONOMY]
  • [DATABASE_TEMPLATE]
  • [DBXREFS]
  • [ENSEMBL]
  • [EXTERNAL_DBS]
  • [FILES]
  • [_DESCRIPTIONS]
  • [_NAMES]
  • [_STABLE_IDS]
  • [GFF]
  • [META]
  • [MODIFY]
  • [SCAFFOLD_NAMES]
  • [XREF]

Configuration Options (Compara Import)

  • [DATABASE_CORE]
  • [DATABASE_COMPARA]
  • [DATABASE_TEMPLATE]
  • [ENSEMBL]
  • [METHOD_LINK]
  • [SPECIES_SET]
  • [TAXA]
  • [ORTHOGROUP]
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[DATABASE_CORE]

Suggest Edits
[DATABASE_CORE]
    HOST = localhost
    PORT = 3306
    RO_USER = anonymous
    RO_PASS =

Connection details for a server hosting species core databases (should usually match [DATABASE_CORE]). NAME does not need to be specified here as a connection will be made for each core database listed in the [TAXA] stanza.

Updated less than a minute ago