[Biopython] question on installation of BioPython on Mac OS 10.7
Jared.Sampson at nyumc.org
Tue Feb 28 21:05:10 UTC 2012
Hi Daria et al. -
What about using pip<http://www.pip-installer.org/en/latest/index.html> or easy_install?
I'm running a Mac with Lion and I had no problem installing Biopython via:
sudo pip install numpy
sudo pip install biopython
I got a "you need numpy first" warning when I tried installing biopython alone, but running the commands above worked just fine to install numpy first, then Bio. It may be useful to note I've done this mainly within a virtualenv<http://www.virtualenv.org/en/latest/index.html>, but I think it should work using the system Python as well.
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Ave MSB 329/398
New York, NY 10016
On Feb 28, 2012, at 12:18 PM, Peter Cock wrote:
On Tue, Feb 28, 2012 at 5:00 PM, Daria Fedyukina <fedyukina at gmail.com<mailto:fedyukina at gmail.com>> wrote:
Thank you. I tried Terminal, it is indeed exactly the same.
NumPy is not installed somehow. Here is my screenshot. Do you have any
suggestions on how to install NumPy in such a way that this installation is
seen when I do "python setup.py build" in the terminal?
Personally I use Apple's provided Python, which from memory
comes with a (slightly out of date) copy of NumPy. A more detailed
reply will have to wait until I'm at my Mac OS X 10.7 "Lion" machine.
If anyone else online right now has Biopython installed and working
on Mac OS X 10.7 "Lion" and can help now, please speak up.
One important question could be was this a clean install of Lion,
or an update from Snow Leopard?
I'm a little confused now even with the screenshots. It looks
like you have download python-2.7.2-macosx10.6.dmg and
numpy-1.6.1-py2.7-python.org-macosx10.3.dmg which should
work fine together BUT you will have two copies of Python (the
Apple provided Python, and Python.org<http://Python.org>'s Python) and it can be
confusing about which is in use and which has a given library
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