On Aug 12, 2014, at 10:15 AM, Sajdak, Doris <djm29@buffalo.edu> wrote:

Hi Nate,
 
Thanks for the fast response.  You were right, python2-6-dev wasn’t installed.  I’m all for using 2.7 and that’s what’s installed on the system but I don’t know how to do that in the virtual environment.  Can you tell me how to switch that?  Sorry if that’s a ridiculously basic question!

Hi Dori,

You can have virtualenv use a specified Python interpreter with the --python argument to virtualenv(.py), by using the VIRTUALENV_PYTHON environment varaible, or by calling virtualenv.py with the desired python interpreter (e.g. `/usr/bin/python2.7 /path/to/virtualenv.py /path/to/venvdir`). See the documentation for more:

    https://virtualenv.pypa.io/en/latest/virtualenv.html#environment-variables-and-configuration-files

--nate

 
Thanks,
Dori
 
 
From: Nate Coraor [mailto:nate@bx.psu.edu] 
Sent: Tuesday, August 12, 2014 10:08 AM
To: Sajdak, Doris
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] can't install numpy from toolshed
 
On Aug 12, 2014, at 9:59 AM, Sajdak, Doris <djm29@buffalo.edu> wrote:


I’m running Galaxy in a virtual environment as described here (OS is Debian 3.2.54-2):
 
When I go to install package_numpy_1_7 from the tool shed, I get the following errors:
 
Running from numpy source directory.
/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/config.py:413: DeprecationWarning:
+++++++++++++++++++++++++++++++++++++++++++++++++
Usage of get_output is deprecated: please do not
use it anymore, and avoid configuration checks
involving running executable on the target machine.
+++++++++++++++++++++++++++++++++++++++++++++++++
 
  DeprecationWarning)
Traceback (most recent call last):
  File "setup.py", line 214, in <module>
    setup_package()
  File "setup.py", line 207, in setup_package
    configuration=configuration )
  File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/core.py", line 186, in setup
    return old_setup(**new_attr)
  File "/usr/lib/python2.6/distutils/core.py", line 152, in setup
    dist.run_commands()
  File "/usr/lib/python2.6/distutils/dist.py", line 975, in run_commands
    self.run_command(cmd)
  File "/usr/lib/python2.6/distutils/dist.py", line 995, in run_command
    cmd_obj.run()
  File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/install.py", line 55, in run
    r = old_install.run(self)
  File "/usr/lib/python2.6/distutils/command/install.py", line 615, in run
    self.run_command('build')
  File "/usr/lib/python2.6/distutils/cmd.py", line 333, in run_command
    self.distribution.run_command(command)
  File "/usr/lib/python2.6/distutils/dist.py", line 995, in run_command
    cmd_obj.run()
  File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/build.py", line 37, in run
    old_build.run(self)
  File "/usr/lib/python2.6/distutils/command/build.py", line 135, in run
    self.run_command(cmd_name)
  File "/usr/lib/python2.6/distutils/cmd.py", line 333, in run_command
    self.distribution.run_command(command)
  File "/usr/lib/python2.6/distutils/dist.py", line 995, in run_command
    cmd_obj.run()
  File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/build_src.py", line 152, in run
    self.build_sources()
  File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/build_src.py", line 169, in build_sources
    self.build_extension_sources(ext)
  File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/build_src.py", line 328, in build_extension_sources
    sources = self.generate_sources(sources, ext)
  File "/ifs/projects/galaxy/database/tmp/tmp-toolshed-mtdaP2Rhs/numpy-1.7.1/numpy/distutils/command/build_src.py", line 385, in generate_sources
    source = func(extension, build_dir)
  File "numpy/core/setup.py", line 410, in generate_config_h
    moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
  File "numpy/core/setup.py", line 41, in check_types
    out = check_types(*a, **kw)
  File "numpy/core/setup.py", line 271, in check_types
    "Cannot compile 'Python.h'. Perhaps you need to "\
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.
 
python-dev is installed on the machine, though I don’t know if that matters in the virtual environment.  Any idea what’s causing this?
 
Hi Dori,
 
Can you check that python2.6-dev is also installed? On Debian Wheezy, python-dev installs the development files for Python 2.7, but your default python appears to be Python 2.6.
 
That said, unless you are using 2.6 intentionally, I would suggest switching to 2.7. Although the Galaxy server and most Galaxy tools written in Python will run in 2.6, some tools now require Python 2.7.
 
--nate
 
 
THANKS!
Dori
 
**********************************
Dori Sajdak
Senior Systems Administrator
State University of NY at Buffalo
Center for Computational Research
701 Ellicott St
Buffalo, NY 14203
Phone: (716) 881-8934
Fax: (716) 849-6656
**********************************
 
 
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