On Mon, Mar 23, 2015 at 4:00 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Mon, Mar 23, 2015 at 1:41 PM, John Chilton <jmchilton@gmail.com> wrote:
Hey Peter,
Thanks for continuing to apply pressure on these issues. I have pushed some logging into Galaxy's development branch (https://github.com/galaxyproject/galaxy/commit/8cb06d7fc2913b4d83ca01b50d76e...) that should make that error more informative. I don't know when that will get pushed out to bitbucket and the shed retested - but once those two things happen we will hopefully have a better idea what the problem is (probably some subtle deployment problem - some incompatible version of samtools on the path? samtools on Galaxy's path but not the test script's path?).
-John
Lovely - I agree this seems the most likely cause, so fingers crossed.
Thank you,
Peter
Sadly this tool hasn't been tested since 2015-03-18 so we don't yet know what extra clues your debug logging will reveal... https://testtoolshed.g2.bx.psu.edu/view/peterjc/samtools_depad/ Peter