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-a... --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): https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use...

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 Web: http://ccr.buffalo.edu **********************************

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