title: Why does pip install biopython fail (but other packages succeed)?
body: <p>I am trying to install python packages in a directory shared by a group of developers.   We do not have sudo permission.   This works for some packages (e.g. seqmagick), but not for others(e.g. biopython).  Can anyone tell me what is different about those that fail. and is there any workaround?</p>
  
  <pre><code>$ pip --version
  pip 1.5.4 from /usr/lib/python2.7/dist-packages (python 2.7)
  </code></pre>
  
  <p>I have created a setup.cfg file like this in the current directory,</p>
  
  <pre><code>[install]
  install-base=/tmp/group/python
  install-purelib=$base/lib
  install-platlib=$base/lib.$PLAT
  install-scripts=/tmp/different/bin
  install-headers=$base/include
  install-data=$base/data
  </code></pre>
  
  <p>The following works, and everything ends up in the right place:</p>
  
  <blockquote>
    <p>$ pip install --no-deps seqmagick</p>
  </blockquote>
  
  <p>But this does not,</p>
  
  <blockquote>
    <p>$ pip install --no-deps biopython</p>
  </blockquote>
  
  <p>The failure is,</p>
  
  <pre><code>running install_lib
  creating /usr/local/lib/python2.7/dist-packages/BioSQL
  error: could not create '/usr/local/lib/python2.7/dist-packages/BioSQL': Permission denied
  </code></pre>
  
  <p>Why would pip (or setup.py?) be installing stuff in /usr/local when the setup.cfg scheme points elsewhere?</p>
  
  <p>Thanks in advance for any insights.</p>