Example: Bowtie (standard external application)

In this example, we show how to integrate Bowtie [Langmead et al., 2009], a popular tool for mapping short sequencing reads to a reference sequence, as a standard external application. Here, two post processing tools will be configured, allowing us to import more than one output generated by bowtie into the CLC Server.

Importing the configuration file provided as an example, and following the instructions in this section, leads to three tools being made available to users logged into the CLC Server via their Workbench or the Command Line Tools: CLC bio Bowtie Build Index, CLC bio Bowtie List Indices and CLC bio Bowtie Map.