I have a Linux with both Python 2.6 and Python 2.7. Apparently Python is so bad 
designed that you cannot simply upgrade from 2.6 to 2.7 without breaking your 
system. As latest Galaxy works with Python 2.7, I put an alias in my .bashrc to 
/usr/local/bin/python2.7 and the same with virtualenv. I also enabled bash 
debugging and enabled expanded alias into .sh scripts.


Then I ran :


$ sh galaxy/run.sh


... lots of output ---

Requirement already satisfied: pysam==0.8.4+gx1 in 
./.venv/lib/python2.7/site-packages (from -r requirements.txt (line 70))
Requirement already satisfied: PasteScript in 
./.venv/lib/python2.7/site-packages (from pulsar-galaxy-lib==0.7.0.dev5->-r 
requirements.txt (line 51))
++ PYTHONPATH=lib
++ /usr/local/bin/python2.7 -c 'import galaxy.dependencies; print 
'\''\n'\''.join(galaxy.dependencies.optional('\''config/galaxy.ini'\''))'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/home/galaxy/galaxy/lib/galaxy/dependencies/__init__.py", line 9, in 
<module>
    from galaxy.util import asbool
  File "/home/galaxy/galaxy/lib/galaxy/util/__init__.py", line 31, in <module>
    from six import binary_type, iteritems, PY3, string_types, text_type
ImportError: No module named six
+ GALAXY_CONDITIONAL_DEPENDENCIES=
+ exit 1


If I check with root user, six package is installed. My guess was I am missing 
an alias to pip2.7, then I added such alias in my .bashrc and again:


$ sh galaxy/run.sh


... lots of output ---

++ '[' -n /bin/bash -o -n '' ']'
++ hash -r
+ unset PYTHONPATH
+ '[' -z /home/galaxy/galaxy/.venv ']'
+ : https://wheels.galaxyproject.org/simple
+ '[' 1 -eq 1 ']'
+ /usr/local/bin/pip2.7 install 'pip>=8.1'
Traceback (most recent call last):
  File "/usr/local/bin/pip2.7", line 5, in <module>
    from pkg_resources import load_entry_point
  File 
"/usr/local/lib/python2.7/site-packages/distribute-0.6.44-py2.7.egg/pkg_resources.py",
 line 2850, in <module>
    working_set.require(__requires__)
  File 
"/usr/local/lib/python2.7/site-packages/distribute-0.6.44-py2.7.egg/pkg_resources.py",
 line 696, in require
    needed = self.resolve(parse_requirements(requirements))
  File 
"/usr/local/lib/python2.7/site-packages/distribute-0.6.44-py2.7.egg/pkg_resources.py",
 line 594, in resolve
    raise DistributionNotFound(req)
pkg_resources.DistributionNotFound: pip==9.0.1


# pip --version
pip 9.0.1 from /usr/local/lib/python2.7/site-packages/pip-9.0.1-py2.7.egg 
(python 2.7)
I have installed Python 2.7 and its tools (virtualenv, pip, etc) following 
official guidelines.


How can install the missing dependecies?


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