Velvet integration
Velvet [Zerbino and Birney, 2008] is a popular de novo assembler for next-generation sequencing data.
The Velvet package includes two programs that need to be run consecutively. The external applications system on the CLC Server is designed to call one program, so a wrapper script is needed to make the needed consecutive calls to the Velvet applications.
An example script as well as a configuration file are available in a zip file at http://www.resources.qiagenbioinformatics.com/external-applications/velvet-example.zip. These will be used to illustrate how this sort of application can be configured as an external application on a CLC Server.
Subsections