On Tue, Nov 12, 2013 at 2:37 PM, John Chilton <chil...@msi.umn.edu> wrote:
> This sounds a lot like this;
> http://dev.list.galaxyproject.org/galaxy-cant-find-binaries-in-tp4662442p4662444.html.
> When using the local job runner (as the test framework likely does), I
> believe samtools needs to be on Galaxy's path. I don't think it is
> enough to just have it available as a "tool dependency" (installed via
> tool shed or not).
> As workarounds Dave could either install the samtools OS package or
> place the tool shed install of this on Galaxy's path before starting?
> .Alternatively, I guess the underlying problem could be solved -
> though it is not entirely clear the best path forward on that, only
> that is a real problem.
> -John

Yes, that sounds like the same problem - and I agree a short term
hack would be to put samtools on the test system.

On Tue, Nov 12, 2013 at 2:35 PM, Greg Von Kuster <g...@bx.psu.edu> wrote:
> Hello Peter,
> Thanks for reporting this - I've added the following Trello card for this 
> issue.
> https://trello.com/c/sN2iLCCn/99-bug-in-install-and-test-framework-1
> Greg Von Kuster

That Trello link seems to be broken for me :(

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