From BioUML platform
- Go to BioUML src directory/db_setup/ensembl
- Edit build.xml there:
- SPECIES: lower-case underscore-separated taxonomical species (homo_sapiens, mus_musculus or rattus_norvegicus)
- VERSION: underscore-separated Ensembl release version for given species (like '71_37'). Visit ftp://ftp.ensembl.org/pub/current_mysql/ to check the latest version available (it's the suffix of the corresponding directory name).
- GENOME_BUILD: Genome build string like 'hg19' or 'mm10'. Leave this empty if you're not sure.
- COLLECTION_NAME: How the resulting database will be named in BioUML installation under 'databases' tab.
- SOURCE_FOLDER: Folder to store downloaded files. Default is "." which means the current folder.
- TARGET_PATH: Path to 'databases' root of BioUML repository. Usually it's a subfolder inside the BioUML installation folder, named 'repo' for BioUML server and 'data' for BioUML workbench.
- DB_HOST: mysql server host to connect to.
- USER, PASS: mysql user and password with administrative privileges.
- Put commons-net-3.3.jar into ant CLASSPATH. See Ant installation manual for details.
- Run ant (with default target “setup”).
ant -lib commons-net-3.3.jar
- Default target will do the following things:
- Download necessary database dumps;
- Create mysql databases named in the same was as in the Ensembl (for example, "homo_sapiens_core_71_37");
- Grant an access to these databases to user 'ensembl' with password 'ensembl';
- Create schema and import database dumps;
- Create repository configuration files.
- If necessary, you may use separate ant targets for downloading, installing or creating configuration files.
- Make sure that created configuration files in repository are accessible for the user which will be used for running BioUML.
- Lucene indexes should be created separately for installed Ensembl. See Lucene indexes creation for details.
- If you use mysql version > 5.6 you should enable compatibility with MySQL 5.6 (version used by ensembl to create dumps). Run in mysql console:
set GLOBAL show_compatibility_56 = ON
SET GLOBAL sql_mode = ;