Jorge, I think that I omitted the igvtools index command because galaxy implicitly manages indexes for datasets as as defined in the datatypes_conf.xml configuration file. I could add the igvtools index command if the galaxy implicit indexing is not sufficient. Thanks, JJ On 1/24/13 9:49 AM, Jorge Sepulveda MD, PhD wrote:

Hi, Jim,

I very much appreciate your galaxy wrappers for igvtools. I was wondering why you did not include the igvtools indexer. I tried to make a wrapper for it but it did not work. Your help will be much appreciated!

Jorge Sepulveda, MD, PhD Associate Director for Laboratory Medicine, Medical Director of Laboratory Informatics, Columbia University Medical Center Associate Professor, Department of Pathology & Cell Biology Columbia University College of Physicians and Surgeons PH1590B 622 W 168 St <x-apple-data-detectors://0> New York, NY 10032 <x-apple-data-detectors://0> Cell: (917) 862-6050 <tel:347-891-1122> Office: 212-305-6360 <tel:212-305-6360> E-mail:jls2282@columbia.edu <mailto:jls2282@columbia.edu>