GenomeHubs
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GenomeHubs
Introduction
Introduction
GenomeHubs
Files and containers
Demo
Quick Start
1. Prepare
2. Setup MySQL database server
(optional) Test Ensembl browser
3. Import assembly and gene models
4. Export files
5. Run analyses
6. Import analysis results
7. Update meta
8. Start download site
9. Start BLAST server
10. Start search container
11. Edit Ensembl plugin
12. Start Ensembl browser
Next Steps
Setup with multiple hosts
Understand the GFF parser
Import additional assemblies
Run comparative analyses
Import variation data
Add track hubs
Connect using Perl API
Set up REST API
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(optional) Test Ensembl browser
At this stage you may wish to start up a basic Ensembl mirror site using the local copy of the Ensembl core database(s) from the previous step. This will lack many of the additional features of a complete GenomeHubs site but provides a useful opportunity to check that the basic components are working before continuing with the instructions to import your own data.

Edit setup.ini

Edit database settings:
  • for the default setup, only DB_SESSION_PASS should need changing
  • database hosts should match the name of your mysql container
  • DB_FALLBACK_HOST is used to allow additional databases to be loaded from a remote host (in this case EnsemblGenomes) so not all databases need to be hosted locally
$ nano ~/genomehubs/v1/ensembl/conf/setup.ini
[DATABASE]
DB_HOST = genomehubs-mysql
DB_PORT = 3306
DB_USER = anonymous
DB_PASS =
​
DB_FALLBACK_HOST = mysql-eg-publicsql.ebi.ac.uk
DB_FALLBACK_PORT = 4157
DB_FALLBACK_USER = anonymous
DB_FALLBACK_PASS =
​
DB_SESSION_HOST = genomehubs-mysql
DB_SESSION_PORT = 3306
DB_SESSION_USER = ensrw
DB_SESSION_PASS = CHANGEME
Set database names to load:
  • Assemblies will be listed on your Ensembl site homepage in the order they are added to SPECIES_DBS
e93
e89
e85
$ nano ~/genomehubs/v1/ensembl/conf/setup.ini
[DATA_SOURCE]
SPECIES_DBS = [
melitaea_cinxia_core_40_93_1
]
$ nano ~/genomehubs/v1/ensembl/conf/setup.ini
[DATA_SOURCE]
SPECIES_DBS = [
melitaea_cinxia_core_36_89_1
]
$ nano ~/genomehubs/v1/ensembl/conf/setup.ini
[DATA_SOURCE]
SPECIES_DBS = [
melitaea_cinxia_core_32_85_1
]

Start the EasyMirror container

Start the EasyMirror Docker container:
e93
e89
e85
$ docker run -d \
--name genomehubs-ensembl \
-v ~/genomehubs/v1/ensembl/conf:/conf:ro \
--network genomehubs-network \
-p 8881:8080 \
genomehubs/easy-mirror:19.05
$ docker run -d \
--name genomehubs-ensembl \
-v ~/genomehubs/v1/ensembl/conf:/conf:ro \
--link genomehubs-mysql \
-p 8081:8080 \
genomehubs/easy-mirror:17.06
$ docker run -d \
--name genomehubs-ensembl \
-v ~/genomehubs/v1/ensembl/conf:/ensembl/conf:ro \
--link genomehubs-mysql \
-p 8081:8080 \
genomehubs/easy-mirror:17.03
Quick Start - Previous
2. Setup MySQL database server
Next - Quick Start
3. Import assembly and gene models
Last modified 2yr ago
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Outline
Edit setup.ini
Start the EasyMirror container