CNVKIT import errors

Question

[alons]

Hi all,

I'm trying to run CNVkit (from source, in linux) after following the installation instructions on the github page but running into import errors which seem to be rare as I couldn't find any references online:

Traceback (most recent call last):
  File "cnvkit.py", line 8, in <module>
    from cnvlib import commands
  File "/home/alon/Desktop/BioinformaticsPrograms/cnvkit/cnvlib/__init__.py", line 4, in <module>
    from .cmdutil import read_cna as read
  File "/home/alon/Desktop/BioinformaticsPrograms/cnvkit/cnvlib/cmdutil.py", line 9, in <module>
    from .cnary import CopyNumArray as CNA
  File "/home/alon/Desktop/BioinformaticsPrograms/cnvkit/cnvlib/cnary.py", line 14, in <module>
    from .segmetrics import segment_mean
ImportError: No module named segmetrics

Will greatly appreciate any help!

Alon

[h.mon]

Try to install using virtualenv and pip, currently (2018-01-22) PyPI hosts the same version as the GitHub repository.

[rashi.naresh]

` I have the sane error:

python ../cnvkit.py import-picard picard/p2-20_5.antitargetcoverage.csv picard/p2-20_5.targetcoverage.csv picard/p2-5_5.antitargetcoverage.csv picard/p2-5_5.targetcoverage.csv picard/p2-9_5.antitargetcoverage.csv picard/p2-9_5.targetcoverage.csv -d build/
Traceback (most recent call last):
  File "../cnvkit.py", line 8, in <module>
    from cnvlib import commands
  File "/Users/rashinaresh/cnvkit/cnvlib/__init__.py", line 4, in <module>
    from .cmdutil import read_cna as read
  File "/Users/rashinaresh/cnvkit/cnvlib/cmdutil.py", line 9, in <module>
    from .cnary import CopyNumArray as CNA
  File "/Users/rashinaresh/cnvkit/cnvlib/cnary.py", line 14, in <module>
    from .segmetrics import segment_mean
ModuleNotFoundError: No module named 'cnvlib.segmetrics'
make: *** [build/reference-picard.cnn] Error 1 `

[julian.dangelo]

Having the same issue as you both. Please post solution if anyone of you figure it out (I will as well).

[ptoru001]

hi all i am having similar errors with installation of cnvkit (for mac)...and cannot seem to figure it out...would anyone kindly please help?

base) torunp01@LEVIND19-I27R5K test % make
python3 ../cnvkit.py import-picard picard/p2-20_5.antitargetcoverage.csv picard/p2-20_5.targetcoverage.csv picard/p2-5_5.antitargetcoverage.csv picard/p2-5_5.targetcoverage.csv picard/p2-9_5.antitargetcoverage.csv picard/p2-9_5.targetcoverage.csv -d build/
Traceback (most recent call last):
  File "../cnvkit.py", line 4, in <module>
    from cnvlib import commands
  File "/Users/torunp01/opt/miniconda3/gatk/cnvkit/cnvlib/__init__.py", line 1, in <module>
    from skgenome.tabio import write
  File "/Users/torunp01/opt/miniconda3/gatk/cnvkit/skgenome/__init__.py", line 1, in <module>
    from . import tabio
  File "/Users/torunp01/opt/miniconda3/gatk/cnvkit/skgenome/tabio/__init__.py", line 10, in <module>
    import pandas as pd
ModuleNotFoundError: No module named 'pandas'
make: *** [build/reference-picard.cnn] Error 1

[GenoMax]

Please use conda to do the installation. A basic tutorial is available here to use conda (use the part for conda): Creating workflows with snakemake and conda

Answer 1

[Eric T.]

This is fixed now. Sorry for the trouble, I forgot to check in a new file while refactoring.

[alons]

Great! Thank you. Seems to be working now, running it.

Answer 2

[WouterDeCoster]

Try the installation with conda. That's likely to solve many of your installation-related issues for many tools.

[julian.dangelo]

After removing all of the cnvkit files associated with the download via pip, I installed conda and used conda to get the cnvkit.py script which then worked fine. Seems that ONLY the conda method of installation works properly.

Thank you for the suggestion WouterDeCoster

[WouterDeCoster]

Conda is going to change how you do your installations. Always try conda first, rather than building stuff manually.

I have moved my comment so you can mark is as 'accepted' and mark this question as solved.

[alons]

I would but I think the developer of CNVkit (Eric T.) would want to see this first, get his input on it, might be a potential bug. He's pretty active in this forum.