BioPython with Macports?

[ewilbanks]

Hi all,

Anyone have an idea how I might fix this? I've installed biopython and dependencies using macports and it seems to have worked. I don't, however, seem to be able to specify the right PYTHONPATH.

Here's where Macports says my package should be!

$ port location py26-biopython
Warning: port definitions are more than two weeks old, consider using selfupdate
Port py26-biopython 1.56_0 is installed as an image in:
/opt/local/var/macports/software/py26-biopython/1.56_0

Any thoughts much appreciated!
Lizzy

[dawe]

Hi Lizzy,
Besides the fact you can install biopython using setuptools (best way to do it!) without messing your system with an additional python installation under /opt/local

$ sudo easy_install -U biopython

I believe you should check that you are using the python installed in /opt/local/bin (or in /opt/local/Library/Frameworks/Python.framework/Versions/2.6/bin), i.e.

$ which python

d

[ewilbanks]

So I tried using easy_install but got some errors that I didn't really understand. Any idea what might be going wrong here?

$ sudo easy_install -U biopython
Password:
Searching for biopython
Reading http://pypi.python.org/simple/biopython/
Reading http://www.biopython.org/
Reading http://biopython.org/DIST/
Best match: biopython 1.56
Downloading http://biopython.org/DIST/biopython-1.56.zip
Processing biopython-1.56.zip
Running biopython-1.56/setup.py -q bdist_egg --dist-dir /tmp/easy_install-4FnbiD/biopython-1.56/egg-dist-tmp-H4avLI
warning: no previously-included files found matching 'Tests/Graphics/*.pdf'
warning: no previously-included files found matching 'Tests/Graphics/*.eps'
warning: no previously-included files found matching 'Tests/Graphics/*.svg'
warning: no previously-included files found matching 'Tests/Graphics/*.png'
warning: no previously-included files matching '*' found under directory 'Tests/UnitTests'
warning: no previously-included files matching '.cvsignore' found under directory '*'
warning: no previously-included files matching '.gitignore' found under directory '*'
warning: no previously-included files matching '*.pyc' found under directory '*'
cc1: error: unrecognized command line option "-Wno-long-double"
error: Setup script exited with error: command 'gcc' failed with exit status 1

It seems that I'm using the /opt/local/bin/python...

[maubp]

So I tried using easy_install but got some errors that I didn't really understand. Any idea what might be going wrong here?
...

Have you installed Apple's XCode (for gcc etc), including the optional the 10.4 headers, as recommended here?: http://biopython.org/wiki/Download

[dawe]

So I tried using easy_install but got some errors that I didn't really understand. Any idea what might be going wrong here?

Assuming you already have a working gcc installation (otherwise you couldn't have installed macports...), that depends on gcc: -Wno-long-double is not a gcc4 flag. You can remove it from $BASECFLAGS variable in /System/Library/Frameworks/Python.framework/Versions/Current/lib/python2.6/config/Makefile (or whatever is the path on your system).

d

[me_myself_andI]

Hi Lizzy,

I've installed biopython and dependencies using macports and it seems to have worked. I don't, however, seem to be able to specify the right PYTHONPATH.

The installation seems to have worked fine. You only have to make sure now to call the Python interpreter which was used for your Biopython installation (which most likely was /opt/local/bin/python2.6. OS X comes bundled with a Python interpreter, but that's not the one which was used.

Try the following

$ /opt/local/bin/python2.6
>>> from Bio import SeqIO

and see if it works.


Andreas