[Biopython-dev] Bio.PopGen and SIMCOAL2 installation

[Peter]

Hi Tiago,

I've just compiled SIMCOAL2 on a Linux machine from
http://cmpg.unibe.ch/software/simcoal2/ (version 2.1.2).  If anyone
else tries this, it required the use of -fpermissive on g++ 4.1.2 to
compile (and gave lots of deprecation warnings, plus some trivial ones
about header files which didn't end with a newline).

The make file specifies the executable name as simcoal2_1_2, however
it does not include an install target, so it is up to the user where
to put the binary (e.g. I used ~/bin/ rather than system wide) and
perhaps what to call it.  The provided pre-compiled binary is also
called simcoal2_1_2.

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 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.

Thanks,

Peter