Mysql administration

MySQL Database Information

MySQL Details

A local copy of the Ensembl database is maintained to speed up Transcription Details. Each API version connects to a specific database version.

Currently: Dev connects to v64 Test connects to v65 Prod connects to v64 v68 is installed as well but v68 moved to mm10 instead of mm9.

MySQL is setup on Stan.

Install a different ensembl version

1. Download files from ensembl FTP site. ftp://ftp.ensembl.org/pub/ then release-VER#
2. Dowload the following folders

     ensembl_production_ver#
     ensembl_website_ver#
     mus_musculus_core_ver#
     mus_musculus_funcgen_ver#
     rattus_norvegicus_core_ver#
     rattus_norvegicus_funcgen_ver#

1. unzip files in each folder
2. create a database that matches each folder name
3. run the .sql script in each file on appropriate database.
4. cd into the folder and run the following:

/usr/local/mysql/bin/mysqlimport -u root -p --fields_escaped_by=\\ mus_musculus_core_65_37 -L *.txt

Change the mus_musculus_core_65_37 to match the database/folder name.