Problems Installing Biopython On Mac

Question

[elmagodelabahia]

I have several problems to get BioPython installed.

First of all, at MAC prompt I have tried to install BioPython as in the tutorial PDF. While doing this, I have a message saying I have to Install Numpy before, so I go for this.

When installing Numpy, it says to me that I need to have Python 2.6 on my MAC (I have already 2.7), so I go to Python website and download this version and try to install it.

When I have Python 2.6 on my computer, I run numpy installer for MAC, withaout any problem (at least, any problem that I can see), so I go back to install BioPython, thinking it will work, but, instead, it says to me that I don't have numpy on my computer...

What can I do? I'm running a bit mad with this.

Thanks a lot

Miguel Ángel

[elmagodelabahia]

Thank you very much.

I will try both and then I will write you back.

I hope I do not have any more problems.

[Peter]

Each version of Python on your machine (e.g. Python 2.6 and 2.7) will have separate libraries.

[mcolic]

Hello,

I am having the same issue, struggling with the installation of biopython. It seemed fine, but when it came to point to include modules from it, then it started telling me 'Bio' module not found. Then I started following the instructions given in this post, but I am not able to install MacPorts, it says:

Could not find a version that satisfies the requirement MacPorts (from versions: )
No matching distribution found for MacPorts |

What do I do know, any other advice or push what to do?

[glihm]

Can you please tell us more about your system? (OS version, which installer did you use for your Python packages, etc...)

Answer 1

[Zach Powers]

I would recommend installing via MacPorts. Once installed you can simply do:

sudo port install py27-biopython
#for python2.7 or below for python 2.6
sudo port install py26-biopython

these will get all dependencies and will avoid any potential 32bit 64bit problems you may encounter with compiling Numpy.

[Cliff Beall]

MacPorts is what worked for me a while ago - by the way, if your institution's firewall blocks rsync like ours, you may need to look at question 1.12 here: https://trac.macports.org/wiki/FAQ

[elmagodelabahia]

While I am waiting for the Enthought Python to answer me, I have tried to install it via MacPorts, but I have problems again. It seems that the installer does not find some file. First, it says to me that Xcode seems not to be installed and after that, at the terminal window I get this:

Computing dependencies for py27-biopythonError: Unable to execute port: can't read "build.cmd": Failed to locate 'make' in path: '/opt/local/bin:/opt/local/sbin:/bin:/sbin:/usr/bin:/usr/sbin' or at its MacPorts configuration time location, did you move it?

Do you know what is happening? How can I fix it?

Thanks a lot once again

Answer 2

[elmagodelabahia]

Finally I got it!!

I had to install Xcode (not as easy as it seems because of my version of MAC OS X).

After that, I installed MacPorts and followed what Zach Powers told me to do.

I was supposed to be finished but I wasn't, so after doing all of this I ran the installation in the way that biopython says it have to be, that means doing:

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

once I have moved into BioPython's folder in my computer.

And That's it!

Thanks a lot

[gui11aume]

Yes, installing Xcode is usually the missing link. In my case, I had to download it from the Mac website, install it and then install the command line tools from the Xcode menu bar (which contains the C compiler gcc).

Answer 3

[Aaron H]

I would suggest trying the Enthought Python distribution, free to academics. It works great for OS X and comes with numpy, scipy, matplotlib, and many other tools including Biopython. The free to all EPDFree version should also come with numpy and scipy but then you will have to install biopython with 'enpkg biopython'