ImportError: No module named scipy.sparse

[Christopher Sheridan]

Hi,

I am apparently having issues with the qiime installation. I attempted to install qiime through both the pip install and qiime-deploy methods, but everytime I check the qiime config file using

print_qiime_config.py -t

I get the following error message: 

chris@Chris-TrustyTahr:~/Bioinformatics/Software/QIIME/qiime-deploy$ print_qiime_config.py -t
Traceback (most recent call last):
  File "/home/chris/Bioinformatics/Software/QIIME/qiime_software/qiime-1.8.0-release/bin/print_qiime_config.py", line 51, in <module>
    raise ImportError, "%s\n%s" % (e,core_dependency_missing_msg)
ImportError: No module named scipy.sparse
See the QIIME Installation Guide: http://qiime.org/install/install.html

Did I miss something? How could I resolve this issue?

Thank you!

Chris

[Katherine Amato]

Hi Chris,

You need to instal scipy. It's pip installable, so just run:

pip install scipy

Best,

Katie

[Christopher Sheridan]

Hi Katie,

Thanks for your reply, but I had already checked and scipy is correctly installed. Just to double check I ran

pip install scipy

but it was indeed already installed.
"chris@Chris-TrustyTahr:~$ pip install scipy
Requirement already satisfied (use --upgrade to upgrade): scipy in /usr/lib/python2.7/dist-packages
Cleaning up..."

Is there any other reason this may be happening?

Thank you,

Chris

[Katherine Amato]

Hi Chris,

Take a look at this thread and see if it helps at all. Different module, but perhaps a similar issue?

https://groups.google.com/forum/#!topic/qiime-forum/TFnNt2J8qzw

Best,

Katie

[Christopher Sheridan]

Hi Katie,

It was indeed such a problem. Thank you!

I am trying to run qiime on Ubuntu 14.04 where the default python version is 3.4. Since qiime expects to run with python2.7 it doesn't work (at least for the scripts I tested so far). I therefore have to call upon the right version of python at the start of every qiime command line and use full paths to the qiime scripts. I am currently trying to see how to use virtualenv to be able to run qiime without listing the full path to each script.

Still working on that.

Cheers,

Chris

[Daniel McDonald]

Hi Chris,

Python 3 is actually a different language that frustratingly shares the same name. Supporting both is something that we likely will do in the future, but it is not trivial. I definitely recommend using virtualenv, and you can specify which specific Python binary to use when creating a new environment.

Best,

Daniel

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