BinSanity-profile under Miniconda/Bioconda

[bostjan...@fe.uni-lj.si]

Dear BinSanity developers,

I am having issues running BinSanity-profile, which is installed throug Miniconda/Bioconda package manager.

Firstly, I noticed that the provided installation of BinSanity does not properly install dependencies.

By trial-and-error inspection I constellated the following list of packages that needs to be installed in the BinSanity environment:

conda create -y -n BinSanity_env python=2.7 numpy pandas mkl matplotlib BinSanity

However, this does not help either. When running BinSanity-profile --help (or without arguments), I get the following error:

============================================================

Traceback (most recent call last):
  File "/biosoft/miniconda/envs/BinSanity_env/bin/Binsanity-profile", line 6, in <module>
    import csv, time, pandas,os
  File "/biosoft/miniconda/envs/BinSanity_env/lib/python2.7/site-packages/pandas/__init__.py", line 42, in <module>
    from pandas.core.api import *
  File "/biosoft/miniconda/envs/BinSanity_env/lib/python2.7/site-packages/pandas/core/api.py", line 10, in <module>
    from pandas.core.groupby.groupby import Grouper
  File "/biosoft/miniconda/envs/BinSanity_env/lib/python2.7/site-packages/pandas/core/groupby/__init__.py", line 2, in <module>
    from pandas.core.groupby.groupby import (
  File "/biosoft/miniconda/envs/BinSanity_env/lib/python2.7/site-packages/pandas/core/groupby/groupby.py", line 49, in <module>
    from pandas.core.frame import DataFrame
  File "/biosoft/miniconda/envs/BinSanity_env/lib/python2.7/site-packages/pandas/core/frame.py", line 74, in <module>
    from pandas.core.series import Series
  File "/biosoft/miniconda/envs/BinSanity_env/lib/python2.7/site-packages/pandas/core/series.py", line 81, in <module>
    import pandas.plotting._core as gfx
  File "/biosoft/miniconda/envs/BinSanity_env/lib/python2.7/site-packages/pandas/plotting/__init__.py", line 11, in <module>
    from pandas.plotting._core import boxplot
  File "/biosoft/miniconda/envs/BinSanity_env/lib/python2.7/site-packages/pandas/plotting/_core.py", line 45, in <module>
    from pandas.plotting import _converter
  File "/biosoft/miniconda/envs/BinSanity_env/lib/python2.7/site-packages/pandas/plotting/_converter.py", line 8, in <module>
    import matplotlib.units as units
  File "/biosoft/miniconda/envs/BinSanity_env/lib/python2.7/site-packages/matplotlib/__init__.py", line 1162, in <module>
    rcParams = rc_params()
  File "/biosoft/miniconda/envs/BinSanity_env/lib/python2.7/site-packages/matplotlib/__init__.py", line 996, in rc_params
    fname = matplotlib_fname()
  File "/biosoft/miniconda/envs/BinSanity_env/lib/python2.7/site-packages/matplotlib/__init__.py", line 840, in matplotlib_fname
    for fname in gen_candidates():
  File "/biosoft/miniconda/envs/BinSanity_env/lib/python2.7/site-packages/matplotlib/__init__.py", line 829, in gen_candidates
    yield os.path.join(six.moves.getcwd(), 'matplotlibrc')
OSError: [Errno 2] No such file or directory

============================================================

This time it seems that the program does not try to access any package that is still not installed.

Would you be so kind to help me resolve this issue.

Thank you in advance and best regards,

Bostjan Murovec

[egrah...@gmail.com]

Hello,

First check that you have all dependencies. I see you do not list having installed featureCounts. Based on those errors it seems a file somewhere is not being generated which could link back to featureCounts not being in your path. 

If that doesn’t work try making sure that the Conda environment you have contains all of the python modules used, this includes  BioPython, subprocess, Argparse, csv, time, and os (although this seems unlikely as these are usually already installed when you create a new python environment). If none of this helps to absolve the issue try checking the version of all dependencies and get back to me on if the issue is resolved by any of these.

-Elaina

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