A suggestion to use #!/usr/bin/env python instead of #!/usr/bin/python

[mingzhi]

It is better to use #!/usr/bin/env python than #!/usr/bin/python, which can give user maximum flexibility to choose the interpreter to use. For example, in our HPC, there exists several versions of python and the default version (/usr/bin/python) is quite old. By loading other versions of python, we can not simply run run_phylo_cnv.py (after appending it to the PATH), but need to run "python scripts_dir/run_phylo_cnv.py".

[snayfach]

Good point - I'll think about doing this and updating the documentation (since users would need to use python run_phylo_cnv.py versus just run_phylo_cnv.py).

Also, did you run into an error when running run_phylo_cnv.py with the old version of python? If so, what is that version?

[snayfach]

Actually, never mind about needing to update the documentation. Users would still be able to use run_phylo_cnv.py

[mingzhi]

The default version of python in our HPC is 2.6.6. I never try to run PhyloCNV using this old version of python, since I need to install all the other packages, which I am not sure will be successful or not. And python 2.7 works fine.

[snayfach]

I've followed your recommendation and am now using #!/usr/bin/env python