Setup MySQL database server

Each assembly in an Ensembl site is stored in a separate MySQL database. GenomeHubs sites host these databases in a MySQL Docker container.

The EasyMirror container is used to configure users and password in the MySQL container and to mirror Ensembl databases from SQL dumps on the Ensembl/EnsemblGenomes ftp sites, making local copies ready to be hosted alongside newly imported data in a GenomeHubs site.

Create a MySQL container

Create a mysql/data directory to allow the databases to be stored outside of the MySQL container:

$ mkdir -p ~/genomehubs/mysql/data

Create a MySQL Docker container to host the Ensembl Databases for your GenomeHub:

  • See hub.docker.com for more information on the MySQL Docker image.
  • Docker sets up a default network bridge, but to simplify connections between containers by using names rather than IP addresses, it is necessary to connect containers to the same named network bridge using --network genomehubs-network.
  • MYSQL_ROOT_HOST='172.16.0.0/255.240.0.0' will allow all other Docker containers on the same machine to connect to the mysql container as root, even if they are on a different Docker network. This is the simplest configuration as it does not matter which of the available subnets the Docker network has been created on, or which IP addresses are assigned to each of the containers. For more security you may wish to check the subnet of your bridge network and/or restrict access to the IP addresses of specific containers.
$ docker run -d \
             --name genomehubs-mysql \
             --network genomehubs-network \
             -v ~/genomehubs/mysql/data:/var/lib/mysql \
             -e MYSQL_ROOT_PASSWORD=CHANGEME \
             -e MYSQL_ROOT_HOST='172.16.0.0/255.240.0.0' \
             -p 3306:3306 \
             mysql/mysql-server:5.5

Log in to MySQL inside the container to increase max_allowed_packet to allow import of large scaffolds:

$ docker exec -it genomehubs-mysql bash
# mysql -u root -p
> set global max_allowed_packet=10000000000;
> exit

Import Ensembl databases

Edit the database.ini configuration file to set passwords for the database users:

  • the DB_ROOT_PASSWORD should match the value of MYSQL_ROOT_PASSWORD in the docker run command above
  • the DB_HOST must match the value of --name in the docker run command above
  • to mirror existing Ensembl databases in your GenomeHub, add the appropriate database names to SPECIES_DBS as a space-separated list (a corresponding database dump must be available at SPECIES_DB_URL)
  • even if you do not wish to mirror any existing databases, at least one database must be specified in SPECIES_DBS for use as a template when importing new data.
$ nano ~/genomehubs/v1/ensembl/conf/database.ini
# (some lines omitted)
[DATABASE]
  DB_SESSION_USER = ensrw
  DB_SESSION_PASS = CHANGEME

  DB_IMPORT_USER = importer
  DB_IMPORT_PASSWORD = CHANGEME

  DB_ROOT_USER = root
  DB_ROOT_PASSWORD = CHANGEME
  DB_PORT = 3306
  DB_HOST = genomehubs-mysql

[DATA_SOURCE]
  SPECIES_DB_URL = ftp://ftp.ensemblgenomes.org/pub/release-40/metazoa/mysql/
  SPECIES_DBS = [ melitaea_cinxia_core_40_93_1 ]

  MISC_DB_URL = ftp://ftp.ensembl.org/pub/release-93/mysql/
  MISC_DBS = [ ensembl_accounts ]
$ nano ~/genomehubs/v1/ensembl/conf/database.ini
# (some lines omitted)
[DATABASE]
  DB_SESSION_USER = ensrw
  DB_SESSION_PASS = CHANGEME

  DB_IMPORT_USER = importer
  DB_IMPORT_PASSWORD = CHANGEME

  DB_ROOT_USER = root
  DB_ROOT_PASSWORD = CHANGEME
  DB_PORT = 3306
  DB_HOST = genomehubs-mysql

[DATA_SOURCE]
  SPECIES_DB_URL = ftp://ftp.ensemblgenomes.org/pub/release-36/metazoa/mysql/
  SPECIES_DBS = [ melitaea_cinxia_core_36_89_1 ]

  MISC_DB_URL = ftp://ftp.ensembl.org/pub/release-89/mysql/
  MISC_DBS = [ ensembl_accounts ]
$ nano ~/genomehubs/v1/ensembl/conf/database.ini
# (some lines omitted)
[DATABASE]
  DB_SESSION_USER = ensrw
  DB_SESSION_PASS = CHANGEME

  DB_IMPORT_USER = importer
  DB_IMPORT_PASSWORD = CHANGEME

  DB_ROOT_USER = root
  DB_ROOT_PASSWORD = CHANGEME
  DB_PORT = 3306
  DB_HOST = genomehubs-mysql

[DATA_SOURCE]
  SPECIES_DB_URL = ftp://ftp.ensemblgenomes.org/pub/release-32/metazoa/mysql/
  SPECIES_DBS = [ melitaea_cinxia_core_32_85_1 ]

  MISC_DB_URL = ftp://ftp.ensembl.org/pub/release-79/mysql/
  MISC_DBS = [ ensembl_accounts ]

Run the database.sh script in a genomehubs/easy-mirror Docker container:

  • this script will set up database users and import databases into your MySQL container based on the information in the database.ini configuration file.
$ docker run --rm \
             --name genomehubs-ensembl \
             --network genomehubs-network \
             -v ~/genomehubs/v1/ensembl/conf:/ensembl/conf:ro \
             genomehubs/easy-mirror:18.10 /ensembl/scripts/database.sh /ensembl/conf/database.ini
$ docker run --rm \
             --name genomehubs-ensembl \
             -v ~/genomehubs/v1/ensembl/conf:/ensembl/conf:ro \
             --link genomehubs-mysql \
             genomehubs/easy-mirror:17.06 /ensembl/scripts/database.sh /ensembl/conf/database.ini
$ docker run --rm \
             --name genomehubs-ensembl \
             -v ~/genomehubs/v1/ensembl/conf:/ensembl/conf:ro \
             --link genomehubs-mysql \
             genomehubs/easy-mirror:17.03 /ensembl/scripts/database.sh /ensembl/conf/database.ini

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