Hello Christopher, The most current version of the BWA wrapper is designed to work with version 0.5.9. This is true if you are pulling from the development repository or the distribution: http://bitbucket.org/galaxy/galaxy-central/src/21138a4a1fea/tools/sr_mapping... http://bitbucket.org/galaxy/galaxy-dist/src/338ead4737ba/tools/sr_mapping/bw... The documentation in our wiki is slightly outdated and does note 0.5.6 - I will correct this today. http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup Perhaps you are running an older version of Galaxy? Support for the newer BWA version was incorporated on 2011-05-09: http://bitbucket.org/galaxy/galaxy-dist/history/tools/sr_mapping/bwa_wrapper... Please let us know if we can help further. It may be best to post this sort of question to the galaxy-dev@bx.psu.edu mailing list in the future, if you are interested in development community feedback (the dev list is for install/development topics). http://galaxyproject.org/wiki/Support Best, Jen Galaxy team On 11/4/11 11:08 AM, Christopher Callaway wrote:

Hi,

I am trying to run Galaxy locally and downloaded BWA but I can’t get it to run. Do I have to use 0.5.6 or can I use 0.5.9? The make command does not work with ver. 0.5.9.

Thanks,

Christopher W. Callaway

University of Utah

Dept. of Pediatrics

Division of Neonatology

417 Wakara Way

#2222

Salt Lake City, UT 84108

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