pysam with easy_install failed

[GoogleCodeExporter]

I use python 2.7 on 64 bit Linux (Cent OS) and have tried to install pysam with 
easy_install in the following way:

$ easy_install pysam

Unfortunately I get the following errors:
tza@zeus: ~/temp $easy_install pyrex
Searching for pyrex
Reading http://pypi.python.org/simple/pyrex/
Reading http://www.cosc.canterbury.ac.nz/~greg/python/Pyrex/
Best match: Pyrex 0.9.9
Downloading
http://www.cosc.canterbury.ac.nz/greg.ewing/python/Pyrex/Pyrex-0.9.9.tar.gz
Processing Pyrex-0.9.9.tar.gz
Running Pyrex-0.9.9/setup.py -q bdist_egg --dist-dir
/tmp/easy_install-GHdxQJ/Pyrex-0.9.9/egg-dist-tmp-ubgNXc
zip_safe flag not set; analyzing archive contents...
Pyrex.Compiler.Scanning: module references __file__
Adding Pyrex 0.9.9 to easy-install.pth file
Installing pyrexc script to /bio1/opt/python/bin

Installed /bio1/opt/python/lib/python2.7/site-packages/Pyrex-0.9.9-py2.7.egg
Processing dependencies for pyrex
Finished processing dependencies for pyrex

tza@zeus: ~/temp $easy_install pysam
Searching for pysam
Reading http://pypi.python.org/simple/pysam/
Reading http://code.google.com/p/pysam/
Reading http://code.google.com/p/pysam/downloads/list
Best match: pysam 0.3
Downloading http://pysam.googlecode.com/files/pysam-0.3.tar.gz
Processing pysam-0.3.tar.gz
Running pysam-0.3/setup.py -q bdist_egg --dist-dir
/tmp/easy_install-2_x1UK/pysam-0.3/egg-dist-tmp-HSnFWH
Traceback (most recent call last):
   File "/bio1/opt/python/bin/easy_install", line 8, in <module>
     load_entry_point('setuptools==0.6c11', 'console_scripts',
'easy_install')()
   File
"/bio1/opt/python/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/setupt
ools/command/easy_install.py",
line 1712, in main
   File
"/bio1/opt/python/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/setupt
ools/command/easy_install.py",
line 1700, in with_ei_usage
   File
"/bio1/opt/python/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/setupt
ools/command/easy_install.py",
line 1716, in <lambda>
   File "/bio1/opt/python/lib/python2.7/distutils/core.py", line 152, in
setup
     dist.run_commands()
   File "/bio1/opt/python/lib/python2.7/distutils/dist.py", line 953, in
run_commands
     self.run_command(cmd)
   File "/bio1/opt/python/lib/python2.7/distutils/dist.py", line 972, in
run_command
     cmd_obj.run()
   File
"/bio1/opt/python/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/setupt
ools/command/easy_install.py",
line 211, in run
   File
"/bio1/opt/python/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/setupt
ools/command/easy_install.py",
line 446, in easy_install
   File
"/bio1/opt/python/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/setupt
ools/command/easy_install.py",
line 476, in install_item
   File
"/bio1/opt/python/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/setupt
ools/command/easy_install.py",
line 655, in install_eggs
   File
"/bio1/opt/python/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/setupt
ools/command/easy_install.py",
line 930, in build_and_install
   File
"/bio1/opt/python/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/setupt
ools/command/easy_install.py",
line 919, in run_setup
   File
"/bio1/opt/python/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/setupt
ools/sandbox.py",
line 62, in run_setup
   File
"/bio1/opt/python/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/setupt
ools/sandbox.py",
line 105, in run
   File
"/bio1/opt/python/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/setupt
ools/sandbox.py",
line 64, in <lambda>
   File "setup.py", line 56, in <module>
ImportError: No module named Cython.Distutils

Original issue reported on code.google.com by mit...@op.pl on 30 Aug 2010 at 10:41

[GoogleCodeExporter]

pysam requires cython/pyrex to be installed

In version 0.4 we will use setuptools and add a requirement for 
cython 0.4 or pyrex as appropriate.

Thanks for bringing this to our attention.

Original comment by andreas....@gmail.com on 10 Sep 2010 at 12:59

• Changed state: Fixed