cvnkit: what is the problem here?

Question

[bk11]

    cnvkit.py access cja.fa -s 10000 -o cja_targetsegment.bed
Traceback (most recent call last):
  File "/home/bkhatri/cnvkit-master/cnvkit.py", line 8, in <module>
    from cnvlib import commands
  File "/gpfs_home/bkhatri/cnvkit-master/cnvlib/__init__.py", line 3, in <module>
    from .commands import *
  File "/gpfs_home/bkhatri/cnvkit-master/cnvlib/commands.py", line 27, in <module>
    from . import (access, antitarget, autobin, batch, call, core, coverage,
  File "/gpfs_home/bkhatri/cnvkit-master/cnvlib/autobin.py", line 11, in <module>
    from . import coverage, samutil
  File "/gpfs_home/bkhatri/cnvkit-master/cnvlib/coverage.py", line 10, in <module>
    from concurrent import futures
ImportError: No module named concurrent

[Kevin Blighe]

Did you try to install each of the modules listed in the traceback?

python -m pip install MyPackage

[Paul]

Hi, what version python do you have - python --version ? And did you install cnvkit from anaconda, pip or git?

[bk11]

Python Version is 2.7.11 I had installed from git. I want to use it in supercomputer. I have added path to this program using command line

export PATH=/home/bkhatri/CNVkit-0.9.0:$PATH

Answer 1

[Eric T.]

To install from source in-place, I recommend using pip install -e . instead of python setup.py. Generally conda is best, but there's a hiccup in creating the conda package for CNVkit 0.9.0 right now.

To install the dependencies manually, here's the comprehensive list:

        'biopython >= 1.62',
        'future >= 0.15.2',
        'futures >= 3.0',
        'matplotlib >= 1.3.1',
        'numpy >= 1.9',
        'pandas >= 0.18.1',
        'pyfaidx >= 0.4.7',
        'pysam >= 0.10.0',
        'reportlab >= 3.0',
        'scipy >= 0.15.0',