Convert a BAM file into a BigWig coverage file. This can be used directly from 
Galaxy for display at UCSC. The advantage over standard Wiggle format is that 
the data is stored in a compressed format and can be retrieved by genome
region. This allows you to view regions of arbitrarily large Wiggle file data
at UCSC while avoiding the upload costs.

The latest version of the bam_to_wiggle.py script is available at:

https://github.com/chapmanb/bcbb/blob/master/nextgen/scripts/bam_to_wiggle.py

Place the script in the same directory as the XML configuration file, or
provide a soft link to it.

This requires:

Python2, version 2.6 or better
pysam (http://code.google.com/p/pysam/)
wigToBigWig from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)