GenDBWiki/AdministratorDocumentation

GenDB Administrator Documentation

As an alternative to using GenDB via the Internet at Bielefeld University, you can also download it and install it at your location. Please read the installation requirements, installing GenDB requires extensive resources and bioinformatics skills. GenDB 2.x has a web user interface (WebUI) for most user interactions. We recommend that annotation teams use that web interface. In addition to this interface GenDB also has a Gtk-1/Gnome-1 based graphical user interface (GUI) that has some added value, but is difficult to install.

• /DependenciesAndRequirements
• /UpdatingFromOlderVersions
• /Installation

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There is more stuff to be written! Here is just a list of topics:

- GenDB setup via Common Execution Environment (CEE)

- installation and configuration

 - Core

 - Apache

 - Gtk

- installing a GenDB patch/bugfix

- upgrading and update

- backup

- sequence db update

- DRMAA and scheduler issues

- Installation

Install GenDB 2.2

go to your CVS bioinfo directory

   cd ~/CVS_HEAD

Checkout the HEAD version of the bridge_install module

   cvs update -dPA bioinfo/bridge_install

call the install.sh script to set up the installation system in the target directory (/vol/gendb-2.2 in this case)

• bioinfo/bridge_install/install.sh /vol/gendb-2.2/

call the script generate_cebitec_config to generate an initial configfile

• bioinfo/seed_stuff/generate_cebitec_config > /vol/gendb-2.2/config

go to bin directory of your installation

cd /vol/gendb-2.2/bin

install the modules from CVS in the following order and activate each of them

./add_cvs_repository -n common -c ../config

./activate_module -n common

./add_cvs_repository -n wrapper -c ../config

./activate_module -n wrapper

./add_cvs_repository -n projectmanagement -c ../config

./activate_module -n projectmanagement ATTENTION: Check the file /vol/gendb-2.2/share/modules.xml for invalid characters! otherwise installation of GOPARC will fail. The xml parser fails to quote '&'

characters in perl code sections 

./add_cvs_repository -n GOPArc -c ../config

./activate_module -n GOPArc

./add_cvs_repository -n gendb -c ../config

./activate_module -n gendb

GlobalConfig.pm.template was completely outdated

reconfigure_module does not work. Templates were not recomputed, reconfigure_module does not feature configuartion files

• fixed*

./add_cvs_repository -n gendb_web -c ../config

./activate_module -n gendb_web

no bridge_install.xml file for gendb_web head

• fixed*

./add_cvs_repository -n GooBS -c ../config

./activate_module -n GooBS

./add_cvs_repository -n SEED -c ../config

./activate_module -n SEED