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 -
Also, Galaxy updates are working fine now.
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
Building dependency shell command for dependency 'bwa'
galaxy.tools WARNING 2013-07-11 17:16:28,429 Failed to resolve dependency on
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
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