Error installing pyani

[cutykaka]

Hello, guys. I installed python Version 3.5.2 to set up pyani. But after performing with pip3 install pyani command, I have an error in the command python setup.py . How can I solve this problem??

[widdowquinn]

I can't really tell without seeing the error message - please could you copy/paste the message, below.

I've just attempted to install pyani in a virtualenv, and it worked correctly. Here's how I did it:

virtualenv test
source test/bin/activate
pip3 install pyani

The pip install step gave me the output:

$ pip3 install pyani
Collecting pyani
  Downloading pyani-0.2.1-py3-none-any.whl (47kB)
    100% |████████████████████████████████| 51kB 998kB/s 
Collecting rpy2 (from pyani)
  Downloading rpy2-2.8.3.tar.gz (186kB)
    100% |████████████████████████████████| 194kB 1.8MB/s 
Collecting pandas (from pyani)
  Downloading pandas-0.19.1-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (11.4MB)
    100% |████████████████████████████████| 11.4MB 104kB/s 
Collecting matplotlib (from pyani)
  Using cached matplotlib-1.5.3-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting seaborn (from pyani)
  Downloading seaborn-0.7.1.tar.gz (158kB)
    100% |████████████████████████████████| 163kB 2.2MB/s 
Collecting scipy (from pyani)
  Using cached scipy-0.18.1-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting biopython (from pyani)
  Downloading biopython-1.68.tar.gz (14.4MB)
    100% |████████████████████████████████| 14.4MB 41kB/s 
Collecting six (from rpy2->pyani)
  Using cached six-1.10.0-py2.py3-none-any.whl
Collecting pytz>=2011k (from pandas->pyani)
  Using cached pytz-2016.7-py2.py3-none-any.whl
Collecting python-dateutil>=2 (from pandas->pyani)
  Downloading python_dateutil-2.6.0-py2.py3-none-any.whl (194kB)
    100% |████████████████████████████████| 194kB 320kB/s 
Collecting numpy>=1.7.0 (from pandas->pyani)
  Using cached numpy-1.11.2-cp35-cp35m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl
Collecting pyparsing!=2.0.0,!=2.0.4,!=2.1.2,>=1.5.6 (from matplotlib->pyani)
  Using cached pyparsing-2.1.10-py2.py3-none-any.whl
Collecting cycler (from matplotlib->pyani)
  Downloading cycler-0.10.0-py2.py3-none-any.whl
Building wheels for collected packages: rpy2, seaborn, biopython
  Running setup.py bdist_wheel for rpy2 ... done
  Stored in directory: /Users/lpritc/Library/Caches/pip/wheels/e8/08/4c/8a2bec94e55df1a2e175d9d352b30770e554fb8378f76a8cde
  Running setup.py bdist_wheel for seaborn ... done
  Stored in directory: /Users/lpritc/Library/Caches/pip/wheels/cb/c8/67/83d615c0ef9b529558525aa521025b183de8c5b156799b091e
  Running setup.py bdist_wheel for biopython ... error
  Complete output from command /Users/lpritc/test/bin/python3.5 -u -c "import setuptools, tokenize;__file__='/private/var/folders/f9/b9snshhs35sb95fd60kt8x5w0000gn/T/pip-build-4cj1ruhf/biopython/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /var/folders/f9/b9snshhs35sb95fd60kt8x5w0000gn/T/tmp9du15fw0pip-wheel- --python-tag cp35:
  running bdist_wheel
  running build
  running build_py

  Numerical Python (NumPy) is not installed.

  This package is required for many Biopython features.  Please install
  it before you install Biopython. You can install Biopython anyway, but
  anything dependent on NumPy will not work. If you do this, and later
  install NumPy, you should then re-install Biopython.

  You can find NumPy at http://www.numpy.org

  ----------------------------------------
  Failed building wheel for biopython
  Running setup.py clean for biopython
Successfully built rpy2 seaborn
Failed to build biopython
Installing collected packages: six, rpy2, pytz, python-dateutil, numpy, pandas, pyparsing, cycler, matplotlib, scipy, seaborn, biopython, pyani
  Running setup.py install for biopython ... done
Successfully installed biopython-1.68 cycler-0.10.0 matplotlib-1.5.3 numpy-1.11.2 pandas-0.19.1 pyani-0.2.1 pyparsing-2.1.10 python-dateutil-2.6.0 pytz-2016.7 rpy2-2.8.3 scipy-0.18.1 seaborn-0.7.1 six-1.10.0

This installed the module and scripts, e.g.:

$ average_nucleotide_identity.py -h
usage: average_nucleotide_identity.py [-h] [-o OUTDIRNAME] [-i INDIRNAME] [-v]
                                      [-f] [-s FRAGSIZE] [-l LOGFILE]
                                      [--skip_nucmer] [--skip_blastn]
                                      [--noclobber] [--nocompress] [-g]
                                      [--gformat GFORMAT] [--gmethod GMETHOD]
                                      [--labels LABELS] [--classes CLASSES]
                                      [-m METHOD] [--scheduler SCHEDULER]
                                      [--workers WORKERS]
                                      [--SGEgroupsize SGEGROUPSIZE]
                                      [--maxmatch] [--nucmer_exe NUCMER_EXE]
                                      [--blastn_exe BLASTN_EXE]
                                      [--makeblastdb_exe MAKEBLASTDB_EXE]
                                      [--blastall_exe BLASTALL_EXE]
                                      [--formatdb_exe FORMATDB_EXE]
                                      [--write_excel] [--rerender]
                                      [--subsample SUBSAMPLE] [--seed SEED]
                                      [--jobprefix JOBPREFIX]

[cutykaka]

when I tried to set up Pyani, everytime has changed the error message like below script.

"Command python setup.py egginfo failed with error code 1 in /tmp/pip-build-0hnh2qp/scipy Storing debug log for failure in /root/.pip/pip.log"

Why did the error message happen? I am looking forward to hearing a helpful reply. Thank you.

[widdowquinn]

The problem appears to be in the attempt to install SciPy, so may not be a problem with pyani.

What does the installation log in /root/.pip/pip.log tell you about the failure (this is indicated as the place to check, in the error message you got)

[widdowquinn]

This thread on StackOverflow might be helpful: http://stackoverflow.com/questions/26575587/cant-install-scipy-through-pip

[widdowquinn]

Issue closed because problem appears to be with scipy installation.