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The Ensembl data is provided on the Ensembl FTP site in the form of tab-delimited text files for importing into MySQL. Go to the appropriate release directory and then to 'mysql'.
E.g. ftp://ftp.ensembl.org/pub/current_mysql/
Each 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.
Regardless of which species you choose to install, for a full installation you will probably want to install the multi-species databases as well. i.e. compara, ensembl_website and ensembl_web_user_db_[[SPECIESDEFS::ENSEMBL_VERSION]].
NB: The FTP site will ideally be laid out as described. If, however, for reasons of space or maintainability, files are not located as described then check the ftp site for README files which should explain where the data can be found.
For each database you have downloaded, cd into the database directory and perform steps 3-5. For illustration, we will use homo_sapiens_core_[[SPECIESDEFS::ENSEMBL_VERSION]]_[[SPECIESINFO::Homo_sapiens:SPECIES_RELEASE_VERSION]] as the database - you need to change this appropriately for each database you install. Remember, you also need to download and install the multi-species databases.
create database homo_sapiens_core_[[SPECIESDEFS::ENSEMBL_VERSION]]_[[SPECIESINFO::Homo_sapiens:SPECIES_RELEASE_VERSION]];
Note that we are using the example MySQL settings of /data/mysql as the install directory, and mysqldba as the database user. Note that here mysqldba is a MySQL account with file access to the database, which is not the same as a system user. See the MySQL documentation for instructions on creating/administering users.
/data/mysql/bin/mysql -u mysqldba homo_sapiens_core_[[SPECIESDEFS::ENSEMBL_VERSION]]_[[SPECIESINFO::Homo_sapiens:SPECIES_RELEASE_VERSION]] < homo_sapiens_core_[[SPECIESDEFS::ENSEMBL_VERSION]]_[[SPECIESINFO::Homo_sapiens:SPECIES_RELEASE_VERSION]].sql
/data/mysql/bin/mysqlimport -u mysqldba --fields_escaped_by=\\ homo_sapiens_core_[[SPECIESDEFS::ENSEMBL_VERSION]]_[[SPECIESINFO::Homo_sapiens:SPECIES_RELEASE_VERSION]] -L *.txtNote that owing to the nature of some of the data in Ensembl it has been necessary to escape the table fields when dumping the MySQL text files. Hence to import successfully, a field escape parameter needs to be specified when using mysqlimport
You have now created and loaded the core Ensembl database for human.
Note that all the databases except the ensembl_web_user_db database only require read access for the website to work. The ensembl_web_user_db requires a MySQL user with delete/insert/update permissions. Also note that because its the only database that the website writes data into, the ensembl_web_user_db has no .table (data) files to download.
NB MySQL needs quite a lot of temporary space to load the databases. It is quite possible that your / tmp directory (which MySQL uses by default) is too small, in which case you might see an Error 28 (use the MySQL tool perror to see what these error numbers mean). Fortunately, you can force MySQL to write temporary files to another location. See the MySQL docs for details: http://dev.mysql.com/doc/refman/5.1/en/temporary-files.html. The simplest solution is to start mysqld with the argument --tmpdir my_spacious_tmp_location.
The Ensembl ftp site now includes a copy of the GO database as ensembl_go_[[SPECIESDEFS::ENSEMBL_VERSION]]. Install this if you want local GO information.
To see information about the recommended mysql server configuration and loading times, please go to this page.
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