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
• /GenDBInstallation

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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

If you are installing to an external destination, you first have to set your CVSROOT variable properly

export CVSROOT=:ext:juser@porta.Genetik.Uni-Bielefeld.DE:/vol/cvs/intern/cvsroot 

Create a directory to install your local GenDB-2.2 version

cd /vol
mkdir gendb-2.2
cd gendb-2.2

Checkout the HEAD version of the bridge_install module

cvs checkout -r HEAD bioinfo/bridge_install

Or update your files if you already checked out a cvs version

cvs update -dPA bioinfo/bridge_install

Call the install.sh script which is located in bioinfo/bridge_install to set up the installation system. Define target directory (/vol/gendb-2.2 in this case).

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

The next step is optional: call the script generate_cebitec_config to generate an initial configfile This will produce the typical settings for sge, datbases and biodbs used at the cebitec environment Please checkout the bioinfo/seed_stuff module as well

. 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 If you want to set the configuration settings interactively via gui ommit the -c param

If the -r param is ommited the HEAD version of the CVS will be used!

./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

Comment: GlobalConfig.pm.template was 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

Comment: 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