Jump to Content
easy importDiscussions
GuidesDiscussions
Discussionseasy import
Guides
GuidesDiscussions
All
Guides
Discussions
Start typing to search…

Get Started

  • Quick start guide
  • Background
  • Description
  • Dockerised setup

Stage 1 - Server Setup

  • Stage 1 requirements
  • Step 1.1: Install dependencies
  • Step 1.2: Setup database connections
  • Step 1.3: git clone ensembl repositories

Stage 2 - Core Import

  • Stage 2 requirements
  • Step 2.1: Fetch/summarise assembly/annotation files
  • Step 2.2: Create database and load sequence data
  • Step 2.3: Prepare the gff file for import
  • Step 2.4: Import gff from prepared file
  • Step 2.5: Verify import
  • Step 2.6: Import additional annotations
  • Step 2.7: Export files
  • Step 2.8: Generate search index

Stage 3 - Web site configuration

  • Step 3.1: Update Ensembl webcode
  • Step 3.2: Reload Ensembl website

Stage 4 - Compara Import

  • Stage 4 requirements
  • Step 4.1: Setup compara database
  • Step 4.2: Import orthogroups

Next steps

  • Viewing your Ensembl instance
  • Using plugins
  • Creating a plugin

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]
Powered by 

Stage 4 requirements

Suggest Edits

At lepbase.org, we have recently finished implementing our own compara analysis for import using easy import and will add a full description of the analysis pipeline soon.

Updated less than a minute ago


Step 3.2: Reload Ensembl website
Step 4.1: Setup compara database
Did this page help you?