There is some conflict between two BWA versions in my Galaxy installation. I 
think it happened during BWA (migrated from core to tool-shed) uninstall and 
then BWA install (installed from tool-shed). So I have two BWA revisions (both 
show same version number) out of which one is working fine. It's hard to tell 
which revision is working as I see the same version tag for both revisions - 
https://www.dropbox.com/s/7ux0xafm9yb6s6h/bwa.png .

Also, Galaxy updates are working fine now.

--
Thanks,
Shantanu

On Jul 11, 2013, at 5:33 PM, Shantanu Pavgi (Campus) wrote:

> 
> 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
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