--- a/bam_to_bigwig/README.txt	Tue Jun 07 16:26:46 2011 -0400
+++ b/bam_to_bigwig/README.txt	Wed Sep 05 21:14:54 2012 -0400
@@ -4,15 +4,31 @@
 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:
+History
+-------
+
+As of v0.1.0, the Galaxy tools uses a revised bam_to_bigwig.py script using
+genomeCoverageBed and bedGraphToBigWig - this approach allows gaps/skpis to
+be excluded from the coverage calculation, which is important for RNA-Seq.
 
+Until v0.0.2, this Galaxy tool used the bam_to_wiggle.py script from
 https://github.com/chapmanb/bcbb/blob/master/nextgen/scripts/bam_to_wiggle.py
+which internally used pysam (and thus samtools) and wigToBigWig from UCSC.
+
+Requirements
+------------
 
-Place the script in the same directory as the XML configuration file, or
-provide a soft link to it.
+If you are installing this tool manually, place the Python script in the
+same directory as the XML configuration file, or provide a soft link to it.
+Ensure the following command line tools are on the system path:
 
-This requires:
+pysam - Python interface to samtools (http://code.google.com/p/pysam/)
+genomeCoverageBed - part of BedTools (http://code.google.com/p/bedtools/)
+bedGraphToBigWig  - from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)
 
-Python2, version 2.6 or better
-pysam (http://code.google.com/p/pysam/)
-wigToBigWig from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)
+Credits
+-------
+
+Original script by Brad Chapman, revisions from Peter Cock including the
+switch to using genomeCoverageBed and bedGraphToBigWig based on the work
+of Lance Parsons.