data/mysql/bin/mysql -u mysqldba homo_sapiens_core_109_38 < homo_sapiens_core_109_38.sql See the MySQL documentation for instructions

Note that here mysqldba is a MySQL account with file access to theĭatabase, which is not the same as a system user.

Note that we are using the example MySQL settings of /data/mysql as the install directory, and

Start a MySQL console session (see the Installing MySQL section above if necessary) and issue theĬreate database homo_sapiens_core_109_38 Įxit the console session, and issue the following command to run the ensembl SQL file, which shouldīe in the directory where you unpacked the downloaded data.

Remember, you also need to download and install the Illustration, we will use homo_sapiens_core_109_38 as the database - you need to change thisĪppropriately for each database you install.

Each table file is gzipped so unpack the data into working directories, keeping separate directories forįor each database you have downloaded, cd into the database directory and perform steps 3-5.

Maintainability, files are not located as described then check the ftp site for README files which shouldĮxplain where the data can be found. NB: The FTP site will ideally be laid out as described. You may optionally want to install the comparative genomics databases as well: ensembl_compara_109 and ensembl_ancestral_109 Regardless of which species you choose to install, you will also need ensembl_ontology_109, ensembl_website_109 and an empty copy of ensembl_accounts - even if you do not use logins, this latter db is needed for session data, e.g. Go to the appropriate releaseĮach database directory contains a data file for each table in that database an SQL file that contains the SQL commands necessary to build that database's table structure and a checksum file (using a UNIX 'sum' utility) so you can verify that the data has downloaded correctly. In the form of tab-delimited text files for importing into MySQL.

The Ensembl data is provided on the Ensembl FTP site

Download phpmyadmin mysqldump