Ensembl installation

This page describes how to install Ensembl database and integrate it with BioUML server or BioUML workbench. The information described here is valid for BioUML 0.9.5 and higher.

• 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

Notes

1. 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.
2. If necessary, you may use separate ant targets for downloading, installing or creating configuration files.
3. Make sure that created configuration files in repository are accessible for the user which will be used for running BioUML.
4. Lucene indexes should be created separately for installed Ensembl. See Lucene indexes creation for details.
5. 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

1. for newer mysql versions replcate datetime default values:

sed -i "s/'0000-00-00 00:00:00'/CURRENT_TIMESTAMP/g" build.xml; for f in */*.sql.gz; do echo $f; zcat $f | sed "s/'0000-00-00 00:00:00'/CURRENT_TIMESTAMP/g" | gzip -c > ${f}.tmp; mv ${f}.tmp $f; done