[Biopython] Installing Biopython on Mac

[Eric Ma]

Hi Ulrich,

To solve your immediate problem, you can try a few things, in order:

1. Go to your Terminal and type (without quotations) "gcc". You might get a
pop-up that says, "The 'gcc' command requires the command line tools."
Accept and proceed from there.
2. If you get a message "clang: error: no input files", then you have gcc
installed. You can double-confirm that gcc is installed by doing "which
gcc" at the command line; it'll likely show something along the lines of
"/usr/bin/gcc".
3. Alternative to steps 1 and 2: type "xcode-select --install" in Terminal,
then follow the prompts.

If you're starting out with Python and BioPython, then I would recommend
installing a distribution of Python that is separate from your system
Python. I have written on my own blog recommending the Anaconda
distribution of Python
<http://www.ericmajinglong.com/2014/09/23/5-great-things-about-the-anaconda-distribution/>.
There are some benefits to doing this: (1) You don't risk breaking the
Python that Apple ships with your Mac; I have nuked my environment before
and wreaked iPhoto on older versions of Mac OS X, totally unexpected. (2)
Anaconda solves the software packaging problem pretty nicely, and you don't
have to type "sudo" when installing packages, with biopython being a simple
"conda install biopython" away, and (3) if you or your group members
progress really far with Python, it'll be a great thing to have isolated
"environments", which Anaconda solves nicely as well.

If you need help getting set up, I can attempt to give more detailed
instructions via email.

Cheers,
Eric
———
This email was written with recycled electrons.

w: http://www.ericmajinglong.com/
a: http://about.me/ericmjl
f: https://www.facebook.com/ericmjl

On Sat, Feb 27, 2016 at 6:39 PM, Melcher, Ulrich <ulrich.melcher at okstate.edu
> wrote:

>  I need help interpreting the instruction "You will need to have installed
> Apple's XCode tools from the App Store …, and then the optional command
> line tools from within the XCode GUI's options menu." from
> http://biopython.org/wiki/Download
> I have no trouble installing the Xcode package, but am unable to locate
> either the tools or the options menu. I am not a developer.
> Ulrich Melcher
> Regents & RJ Sirny Professor
> Department of Biochemistry & Molecular Biology
> Oklahoma State University
>
>
> _______________________________________________
> Biopython mailing list  -  Biopython at mailman.open-bio.org
> http://mailman.open-bio.org/mailman/listinfo/biopython
>
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