View source for 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 [http://ant.apache.org/manual/install.html Ant installation manual] for details.
* Run ant (with default target “setup”).
<code>ant -lib commons-net-3.3.jar</code>

=== Notes ===
#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:
<code>set GLOBAL show_compatibility_56 = ON</code>

<code>SET GLOBAL sql_mode = '';</code>

[[Category:Installation]]