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. -- Thanks, Shantanu