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.

• Dependencies and Requirements
• GenDB Installation
• GenDB Installation FAQ
• Updating from older Versions

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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)

- installing a GenDB patch/bugfix

- upgrading and update

- backup

- sequence db update

- DRMAA and scheduler issues

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Installing GenDB-2.2 from CVS

If you are installing from an external destination and have an account for the Center for Biotechnology (CeBiTec), you first have to set your CVSROOT variable properly:

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

Go to a directory of your choice where you would like to install all software modules (you should have approximately 10 MB free disk space), e.g.:

cd /vol

Create a directory to install your local GenDB-2.2 version:

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 have 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 the target directory for the installation (/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 configuration file. This will produce the typical settings for SUN Grid Enginge (SGE), SQL databases and sequence databases used at CeBiTec.

Please checkout the bioinfo/seed_stuff module as well:

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

If you cannot or don't want to use the CeBiTec configuration, create an empty configuration file, e.g.:

/vol/gendb-2.2/> touch config

Go to the bin directory of your installation directory:

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