Question: CNVKIT import errors
1
gravatar for alons
20 months ago by
alons270
Rehovot
alons270 wrote:

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

linux cnv python cnvkit • 1.1k views
ADD COMMENTlink modified 20 months ago by Eric T.2.5k • written 20 months ago by alons270
1

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

ADD REPLYlink written 20 months ago by h.mon27k
1

` 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 `
ADD REPLYlink modified 20 months ago by WouterDeCoster40k • written 20 months ago by rashi.naresh10
1

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

ADD REPLYlink written 20 months ago by julian.dangelo20
2
gravatar for Eric T.
20 months ago by
Eric T.2.5k
San Francisco, CA
Eric T.2.5k wrote:

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

ADD COMMENTlink written 20 months ago by Eric T.2.5k

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

ADD REPLYlink written 20 months ago by alons270
2
gravatar for WouterDeCoster
20 months ago by
Belgium
WouterDeCoster40k wrote:

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

ADD COMMENTlink written 20 months ago by WouterDeCoster40k
1

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

ADD REPLYlink written 20 months ago by julian.dangelo20
1

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.

ADD REPLYlink written 20 months ago by WouterDeCoster40k

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.

ADD REPLYlink modified 20 months ago • written 20 months ago by alons270
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