Derek: Just to let you know that I just wrapped BAMTools for Galaxy: GitHub -> https://github.com/nekrut/bamtools GalaxyToolShed -> https://toolshed.g2.bx.psu.edu/view/anton/bamtools Galaxt Test Server -> https://test.galaxyproject.org (look for BAMTools on the left pane). We will roll them out on the main site soon. Thanks for a great package! anton -- Anton Nekrutenko Professor of Biochemistry and Molecular Biology http://nekrut.bx.psu.edu (814) 826-3051