[Biopython] Problems with Phylo/PAML/codeml.py in newer BioPython version

[Brandon Invergo]

Hi Jeremy,

On Thu, 2016-03-17 at 20:52 -0700, Jeremy Chase wrote:
> Traceback (most recent call last):
>   File "codemlscript.py", line 117, in <module>
>     results = cml.run()
>   File "/usr/local/lib/python2.7/dist-packages/Bio/Phylo/PAML/codeml.py", line 186, in run
>     Paml.run(self, ctl_file, verbose, command)
>   File "/usr/local/lib/python2.7/dist-packages/Bio/Phylo/PAML/_paml.py", line 145, in run
>     stdout=subprocess.PIPE)
>   File "/usr/lib/python2.7/subprocess.py", line 522, in call
>     return Popen(*popenargs, **kwargs).wait()
>   File "/usr/lib/python2.7/subprocess.py", line 710, in __init__
>     errread, errwrite)
>   File "/usr/lib/python2.7/subprocess.py", line 1327, in _execute_child
>     raise child_exception
> OSError: [Errno 2] No such file or directory

It looks like codeml isn't in your PATH.  Verify that you can run it
from the commandline.  Alternatively, you can use the "command" option
to the "run" method to manually specify the location of the codmel
binary.

-brandon