[Biopython-dev] Bio.PopGen and SIMCOAL2 installation

[Tiago Antão]

Hi,

On Mon, Nov 3, 2008 at 12:43 PM, Peter <biopython at maubp.freeserve.co.uk> wrote:
> However, Bio.PopGen.SimCoal.Controller seems to assume the executable
> will be called just simcoal2 (or simcoal2.exe on Windows), and thus
> fails detect a binary called simcoal2_1_2.  The unit test however is
> more flexible and looks for any binary on the path whose name starts
> with simcoal2.  Ideally these two should be consistent.

I am aware of this, in fact, this issue is documented in the tutorial
(9.5.2.2). The idea is that the binary should be called simcoal2 as
documented. This can be changed of course. My preference would be to
change just the test code. Is this ok with you?

> I can make test_PopGen_SimCoal.py pass by installing SIMCOAL2 as
> simcoal2 rather than simcoal2_1_2, but is this a SIMCOAL2 installation
> issue or a bug in Bio.PopGen.SimCoal.Controller?  In my experience it
> is not normal for a Linux tool to include the full version in the
> executable name - using just simcoal2 does make more sense.

Agree. And, again, this is documented in the tutorial. I can go ahead
and change the test code (please just confirm).