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I'm trying to install the biopython module on my Ubuntu 12.04 LTS machine (64x). I first upgraded to Python3.3 by installing from source (biopython does not support other versions), that seems ok.

However, I installed some modules using the sudo apt-get install python-module command but I can't call them from a python shell:

dovah@AsusX501A:~$ python3.3
Python 3.3.5 (default, Mar 12 2014, 02:09:17)
[GCC 4.6.3] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from biopython import *
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named 'biopython'
>>> from Bio import * ##as suggested in http://biopython.org/DIST/docs/api/module-tree.html
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
ImportError: No module named 'Bio'

As you can see, the modules are installed:

dovah@AsusX501A:~$ sudo apt-get install python-biopython
Reading package lists... Done
Building dependency tree      
Reading state information... Done
python-biopython is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

And so is biopython (quite strange though: line 14 says biopython-1.64-py2.7-linux-x86_64.egg so best hit was found for version 2.7, not 3.3):

dovah@AsusX501A:~$ sudo easy_install -f http://biopython.org/DIST/ biopython
Searching for biopython
Reading http://biopython.org/DIST/
Best match: biopython 1.64
Downloading http://biopython.org/DIST/biopython-1.64.zip
Processing biopython-1.64.zip
Writing /tmp/easy_install-v5LJZz/biopython-1.64/setup.cfg
Running biopython-1.64/setup.py -q bdist_egg --dist-dir /tmp/easy_install-v5LJZz/biopython-1.64/egg-dist-tmp-TruGJH
warning: no previously-included files matching '.cvsignore' found under directory '*'
warning: no previously-included files matching '*.pyc' found under directory '*'
zip_safe flag not set; analyzing archive contents...
Bio.Entrez.Parser: module references __path__
Adding biopython 1.64 to easy-install.pth file
Installed /usr/local/lib/python2.7/dist-packages/biopython-1.64-py2.7-linux-x86_64.egg
Processing dependencies for biopython
Finished processing dependencies for biopython

Are modules specific for a given Python version? Is the system still stuck on Python 2.7? Obviousely I can't simply remove 2.7 unless I want to mess up my whole OS.

Thank you in advance for your help.

EDIT numpy successfully installed using: sudo apt-get install python3-numpy

share|improve this question

2 Answers 2

Usually python-* packages are targeted to Python 2.X. The ones to Python 3 are named python3-*.

In your case the package you need is not available, so you will need to install it "manually".

This can be easily achieved with the following:

$ sudo apt-get install python3-dev python3-pip
$ sudo pip3 install biopython

If you dont want it to be installed system-wide you can use a virtualenv:

$ virtualenv -p python3.3 some_location  # replace 3.3 with your version. 
$ source some_location/bin/activate
$ pip install biopython # python3-dev should be already installed.
share|improve this answer
    
I tried your suggestion, but on sudo pip3 install biopython I get the following error: Cleaning up... Command python setup.py egg_info failed with error code 1 in /tmp/pip_build_root/biopython Storing debug log for failure in /home/dovah/.pip/pip.log. It seems not detecting my installed version 3.3 –  Dovah Jul 22 at 13:47
    
Other remark: my system is running on 12.04LTS, so I had to sudo apt-get install python3-setuptools & sudo easy_install3 pip3 (python3-pip isn't available for distros before 13.04) –  Dovah Jul 22 at 13:50
    
Can you post the output in ~/.pip/pip.log? –  Salem Jul 22 at 13:55
    
Actually, bash: cd: /home/dovah/.pip/pip.log: Not a directory –  Dovah Jul 22 at 14:03
    
Sorry, what I meant was the contents of the file: cat ~/.pip/pip.log. –  Salem Jul 22 at 14:07

Works perfectly, check it out. First command:

sudo apt-get install python3-pip

Second command:

pip3 install biopython
root@saurabh-ubuntu:/home/saurabh# apt-get install python-pip python3-pip
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following extra packages will be installed:
  libexpat1-dev libpython3-dev libpython3.4-dev python-colorama python-distlib
  python-html5lib python-requests python-setuptools python-urllib3
  python3-colorama python3-dev python3-distlib python3-html5lib
  python3-setuptools python3.4-dev
Suggested packages:
  python-genshi
Recommended packages:
  python-dev-all
The following NEW packages will be installed:
  libexpat1-dev libpython3-dev libpython3.4-dev python-colorama python-distlib
  python-html5lib python-pip python-requests python-setuptools python-urllib3
  python3-colorama python3-dev python3-distlib python3-html5lib python3-pip
  python3-setuptools python3.4-dev
0 upgraded, 17 newly installed, 0 to remove and 0 not upgraded.
Need to get 28.6 MB of archives.
After this operation, 48.0 MB of additional disk space will be used.
Do you want to continue? [Y/n] y
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Get:4 http://mirror.team-cymru.org/ubuntu/ trusty/universe python-colorama all 0.2.5-0.1ubuntu1 [18.3 kB]
Get:5 http://mirror.team-cymru.org/ubuntu/ trusty/universe python-distlib all 0.1.8-1 [113 kB]
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Get:11 http://mirror.team-cymru.org/ubuntu/ trusty/universe python3-colorama all 0.2.5-0.1ubuntu1 [11.9 kB]
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Get:14 http://mirror.team-cymru.org/ubuntu/ trusty/universe python3-distlib all 0.1.8-1 [113 kB]
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Get:16 http://mirror.team-cymru.org/ubuntu/ trusty/main python3-setuptools all 3.3-1ubuntu1 [144 kB]
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Fetched 28.6 MB in 2min 18s (207 kB/s)                                         
Selecting previously unselected package libexpat1-dev:amd64.
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root@saurabh-ubuntu:/home/saurabh# pip3 install biopython
Downloading/unpacking biopython
  Downloading biopython-1.64.tar.gz (11.7MB): 11.7MB downloaded
  Running setup.py (path:/tmp/pip_build_root/biopython/setup.py) egg_info for package biopython

    warning: no previously-included files matching '.cvsignore' found under directory '*'
    warning: no previously-included files matching '*.pyc' found under directory '*'
Installing collected packages: biopython
  Running setup.py install for biopython
    building 'Bio.cpairwise2' extension
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.4m -c Bio/cpairwise2module.c -o build/temp.linux-x86_64-3.4/Bio/cpairwise2module.o
    x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.4/Bio/cpairwise2module.o -o build/lib.linux-x86_64-3.4/Bio/cpairwise2.cpython-34m.so
    building 'Bio.trie' extension
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -IBio -I/usr/include/python3.4m -c Bio/triemodule.c -o build/temp.linux-x86_64-3.4/Bio/triemodule.o
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -IBio -I/usr/include/python3.4m -c Bio/trie.c -o build/temp.linux-x86_64-3.4/Bio/trie.o
    x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.4/Bio/triemodule.o build/temp.linux-x86_64-3.4/Bio/trie.o -o build/lib.linux-x86_64-3.4/Bio/trie.cpython-34m.so
    building 'Bio.Nexus.cnexus' extension
    x86_64-linux-gnu-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -fPIC -I/usr/include/python3.4m -c Bio/Nexus/cnexus.c -o build/temp.linux-x86_64-3.4/Bio/Nexus/cnexus.o
    x86_64-linux-gnu-gcc -pthread -shared -Wl,-O1 -Wl,-Bsymbolic-functions -Wl,-Bsymbolic-functions -Wl,-z,relro -Wl,-Bsymbolic-functions -Wl,-z,relro -g -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 build/temp.linux-x86_64-3.4/Bio/Nexus/cnexus.o -o build/lib.linux-x86_64-3.4/Bio/Nexus/cnexus.cpython-34m.so

    warning: no previously-included files matching '.cvsignore' found under directory '*'
    warning: no previously-included files matching '*.pyc' found under directory '*'
Successfully installed biopython
Cleaning up...
root@saurabh-ubuntu:/home/saurabh# python3
Python 3.4.0 (default, Apr 11 2014, 13:05:11) 
[GCC 4.8.2] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import Bio
>>> 
[3]+  Stopped                 python3
root@saurabh-ubuntu:/home/saurabh# 
share|improve this answer
    
pip successfully downloaded, executed and installed. However, I get sudo: pip-3.3: command not found for the biopython installation. –  Dovah Jul 22 at 14:07
    
then try sudo pip3 install biopython –  Saurabh Jul 22 at 14:08
    
I get errors. Please refer to my comments on @Salem's answers to this question. –  Dovah Jul 22 at 14:15
    
The name of the module is Bio. So use import Bio –  Saurabh Jul 22 at 14:23
    
As you can see in my posted question, Bio isn't recognized as module under python3.3. And it isn't configured for python3.2, which I installed from Synaptic. I had to upgrade, so I installed version 3.3 from source because Synaptic doesn't include it. So maybe this is the main problem. In fact, /usr/bin/python3 gives me back python3.2 by default. Any ideas for fixing this? –  Dovah Jul 22 at 14:28

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