On Tue, Nov 12, 2013 at 2:37 PM, John Chilton firstname.lastname@example.org wrote:
This sounds a lot like this; http://dev.list.galaxyproject.org/galaxy-cant-find-binaries-in-tp4662442p466....
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.
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 email@example.com wrote:
Thanks for reporting this - I've added the following Trello card for this issue.
Greg Von Kuster
That Trello link seems to be broken for me :(