This guide describes how to install this dbNP module. Installation can be done from source code or using a pre-built WAR file. The method using a WAR file is much easier. However, using the source code you can perform your own changes to the source code, before installation.


This dbNP module needs a working GSCF instance to connect with. You can install GSCF using instructions on GSCF and the module may be on the same server, but this is not required.

The dbNP module can be most easily installed in a tomcat container. See for more information about setting up a tomcat container.

Finally, the module needs a functioning database. PostgreSQL and MySQL database are supported out of the box. If you want support for other databases, you should add the libraries required to the source code, and build a war. See next chapter for more information

Retrieving and adjusting source code

The mass sequencing module has been written in Grails ( You can obtain the source code from SVN using the following command

  svn co dbnp-metagenomics

Write access to the repository is only available to registered developers.

After checking out the source code, you can edit the code and make adjustments. When you are finished editing, use the grails command

  grails war

to create a WAR package for installation. See also for more information. See

Retrieving pre-build package

Go to and download the latest package for this module.

Installing the package

When you have obtained or created a WAR package, you should deploy the package to a tomcat container. You can do so by copying the WAR to the TOMCAT_HOME/webapps directory. See also for more information.

Configuring the package

You can configure the package by editing the file


where [environment] will be the environment the war has been created for. Normally this will be 'www'. If you have created your own package, the environment name might be different.

See Configuration for more information about the configuration.

Checking installation

After your module has been installed and configured, you can check whether the module works properly by going to the URL of the module with a web browser. You should see a login page in GSCF (if you are not logged into GSCF) or a screen indicating there are no runs yet (if you are already logged into GSCF).

Associating the module with GSCF

In order to use the module with data from GSCF, you should add a so called AssayModule? in GSCF. This can only be done as an administrator (using the menu Admin -> Manage modules). See the GSCF documentation for more information.

Last modified 10 years ago Last modified on Jul 25, 2011, 8:49:50 AM