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/bwa_wrapper.py
http://bitbucket.org/galaxy/galaxy-dist/src/338ead4737ba/tools/sr_mapping/bwa_wrapper.py
The documentation in our wiki is slightly outdated and does note 0.5.6 -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.py
Please let us know if we can help further. It may be best to post this
sort of question to the galaxy-...@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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___________________________________________________________
The Galaxy User list should be used for the discussion of
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