trying to install Biopython on Fedora 21, Python 2.7. I've done the following
[mike@localhost Downloads](17:32)$ sudo pip2.7 install biopython
You are using pip version 6.1.1, however version 7.1.0 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Collecting biopython
/usr/lib/python2.7/site-packages/pip/_vendor/requests/packages/urllib3/util/ssl_.py:79: InsecurePlatformWarning: A true SSLContext object is not available. This prevents urllib3 from configuring SSL appropriately and may cause certain SSL connections to fail. For more information, see https://urllib3.readthedocs.org/en/latest/security.html#insecureplatformwarning.
InsecurePlatformWarning
Downloading biopython-1.65.tar.gz (12.6MB)
100% |████████████████████████████████| 12.6MB 33kB/s
Installing collected packages: biopython
Running setup.py install for biopython
Successfully installed biopython-1.65
And then
[mike@localhost Downloads](17:32)$ ipython
Python 2.7.9 |Anaconda 2.2.0 (64-bit)| (default, Mar 9 2015, 16:20:48)
In [1]: import Bio
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-1-a7440e1156be> in <module>()
----> 1 import Bio
ImportError: No module named Bio
What am I doing wrong?
EDIT
I tried installing biopython using
sudo easy_install -f http://biopython.org/DIST/ biopython
and it installed it into /usr/lib/python2.7/site-packages/biopython-1.65-py2.7-linux-x86_64.egg/. Didn't work.
Then I tried installing it using the same command, without the sudo:
easy_install -f http://biopython.org/DIST/ biopython
which installed it into /home/mike/anaconda/lib/python2.7/site-packages/biopython-1.65-py2.7-linux-x86_64.egg
And that worked! Both for ipython and python. But why did it work...?
It's not good practice to sudo pip
, since it may install things under root permission, which is usually not granted to ordinary program.
The problem probably lies in library path. The most informative tools will be
import sys
print (sys.path)
and
which python
pip --version
And use pip install biopython --user
to replace sudo pip