I had migrated BWA tool while at release_2013.02.08 revision. It was working 
fine, however, it fails to run with following warning message after updating 
Galaxy to release_2013.06.03.

Building dependency shell command for dependency 'bwa'
galaxy.tools WARNING 2013-07-11 17:16:28,429 Failed to resolve dependency on 
'bwa', ignoring

The bwa tool dependency is installed and present on the system. I am not sure 
why it's not being detected after the update. I can fix it by sourcing env.sh 
file before starting Galaxy server process, but that's not a good solution. Any 
pointers on resolving this issue would be really helpful.

Also, Galaxy is unable to fetch latest update for the bwa_wrapper. The 
migration script had installed first release of the bwa_wrapper, but now there 
is an updated revision available. I tried getting updates, but Galaxy thinks 
it's current bwa revision is up to date.

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