[Biopython] question on installation of BioPython on Mac OS 10.7

[Sampson, Jared]

Hi Daria -

If the output of typing:

    which easy_install

in a terminal window gives a path, then you have easy_install on your machine already. So you could just type:

    sudo easy_install pip

When that finishes, run the commands from before to install numpy and biopython.

Pip and easy_install are both Python package managers, and the choice of one over the other is largely a matter of preference.  So if you'd rather not install pip, you could replace "pip install" with "easy_install" in those previous commands.

If that doesn't work (i.e. you don't have easy_install either), you can install pip or setuptools (which includes easy_install) by following the instructions on this website<http://www.pip-installer.org/en/latest/index.html> I gave the link to before, under 'installation instructions.'

Hope that helps,

Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Ave MSB 329/398
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/

On Feb 29, 2012, at 12:30 PM, Daria Fedyukina wrote:

Thank you Jared,

I tried to use these commands but it does not know what "pip" is.
I used with no "pip", but it did not help.

I will keep searching for the cure :)

-Daria


On Feb 28, 2012, at 3:05 PM, Sampson, Jared wrote:

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.

Jared


--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
550 First Ave MSB 329/398
New York, NY 10016
212-263-7898
http://kong.med.nyu.edu/

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:

Hi Peter,

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?

-Daria

Hi Daria,

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
installed

Peter
_______________________________________________
Biopython mailing list  -  Biopython at lists.open-bio.org<mailto:Biopython at lists.open-bio.org>
http://lists.open-bio.org/mailman/listinfo/biopython


------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================



------------------------------------------------------------
This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email.
=================================