Dockerised setup

Jump to Content

Guides Discussions

Guides

Guides Discussions

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