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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/