GenDBWiki/AdministratorDocumentation/GenDBInstallationFAQ

Frequently asked questions (FAQ) about installing and setting up GenDB 2.2

Database setup and requirements

• The installation fails due to insufficient permissions on the database server for "gendb@localhost".

  The installation systems creates several user accounts on the database server. It does not specify the host name to allow the web server and command line script to be used within a network (e.g. a dedicated database server and a dedicated web server). The default setup of MySQL often already contains an account for "%@localhost". This account has precedence over the ones generated by the installation system (see also the MySQL privilege system documentation). You have to remove this account prior to installing GenDB 2.2.

Downloads during the installation

• During the installation a number of files are downloaded. What are these files ?

  The GOPArc component stores a number of classification schemes and information about metabolic pathways from the KeGG database. The license for these information does not allow us to bundle the files with GenDB 2.2. The installation system has to download the to build the GOPArc database. The files are:

• COG and KOG from NCBI ([1])
• the compound, enzyme and reaction files from KeGG ligand database ([2])
• the reference maps from the KeGG pathway database ([3])
• I already have these files. How can i skip the download ?

 The current release does not support skipping the download if the files are already available. Some of the files have to be postprocessed during the installation (e.g. correct headers for the COG blastable database). The GOPArc component also expects the files to be available in certain locations within the installation directory. But we may change the download and conversion scripts in a later release to support locally available files.