bioperl/bioperl-run — pull request #13 by hettling (2014-10-29 16:55:35+00:00)
Title: Raxml module did not pass test and -w option only worked with cwd

(1) Test for Raxml wrapper does not pass, as Raxml complains about a starting tree and gives an assertion (tested on linux and mac). This was fixed by starting from a random tree (-d option in Raxml).
(2) Cannot use -w option, since the wrapper throws an error if the Raxml output file is not in the current working directory. This was fixed and a test was added to check if custom working directories (such as /tmp/) work.
(3) Redirect for -quiet option made Raxml write to the wrong file (for some reason). Redirecting was changed.

I would be very happy if these changes could be incorporated,

Best Regards

Hannes Hettling