Question for Biopython Installation on Mac OS X

Question

[qiutianlei0924]

hi,

I have installed python 2.7.5 and Xcode.

How can I install Biopython? I'm not familiar with the UNIX system and I can't understand the "Installing on UNIX and Mac OS X" text.

Can I get a 'step by step' protocol for installation?

Thanks!

Qiu Tianlei

2014.4.28

[Neilfws]

If you are not familiar with UNIX, the shell etc., you will not even be able to use Biopython. So I'd suggest not installing it until you have the required experience and education.

[Peter]

@Neilfws Well, you can use Biopython just fine on Windows - but certainly familiarity with Unix/Linux and the shell is important.

@qiutianlei0924 Have you installed the optional XCode command line utilities as per the Biopython instructions?

[qiutianlei0924]

YES, I have Xcode installed and downloaded Biopython-1.63.tar.gz, but I don't know let the file installed with Xcode.

Answer 1

[Michael]

Please be more specifc, what do you mean by "I can't understand the ... text", what have you tried, where did you get stuck? The installation instructions already contain a step-step manual for different OS's. You can't ask anyone to just type in a complete instruction and MacOS tutorial tailored for you, where should they start, who'd have the time if there is a good manual already? You first need to learn the basics of MacOS, the shell, and UNIX commands. You can't program efficiently if you don't know the basics of the shell.

Also, installation should be extremely easy, did you try:

$ easy_install -f http://biopython.org/DIST/ biopython

Answer 2

[Peter]

Have your read http://biopython.org/wiki/Download yet? You will need to have installed Apple's XCode tools from the App Store (it is a big download), and then the optional command line tools from within the XCode GUI's options menu, or on Mavericks by using the command:

xcode-select --install

Then, in theory, it would just be:

python setup.py build
python setup.py test
sudo python setup.py install

However, there is a potential catch. The last XCode update introduced an incompatibility with the Apple provided Python - this works for some people:

export CFLAGS=-Qunused-arguments
export CPPFLAGS=-Qunused-arguments
python setup.py build
python setup.py test
sudo python setup.py install

For more details see e.g. http://lists.open-bio.org/pipermail/biopython-dev/2014-April/011240.html - an alternative is to install an official (non-Apple modified) Python from http://python.org - useful if for example you might want to use Python 3.3 or 3.4?

[qiutianlei0924]

Thanks for so many details. I will try it.