Dear All
I had a problem to use Jupyter Notebook; I solved it,
Now I am facing a to use ipyrad
Error is:
(base) bash-5.0$ ipyrad
Traceback (most recent call last):
File "/Library/Frameworks/Python.framework/Versions/3.7/bin/ipyrad", line
11, in <module>
load_entry_point('ipyrad==0.1.32', 'console_scripts', 'ipyrad')()
File
"/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pkg_resources/__init__.py",
line 489, in load_entry_point
return get_distribution(dist).load_entry_point(group, name)
File
"/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pkg_resources/__init__.py",
line 2793, in load_entry_point
return ep.load()
File
"/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pkg_resources/__init__.py",
line 2411, in load
return self.resolve()
File
"/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/pkg_resources/__init__.py",
line 2417, in resolve
module = __import__(self.module_name, fromlist=['__name__'], level=0)
File
"/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ipyrad/__init__.py",
line 4, in <module>
from . import load
File
"/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ipyrad/load/__init__.py",
line 16, in <module>
from .load import load_assembly
File
"/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ipyrad/load/load.py",
line 13, in <module>
from ipyrad.core.assembly import Assembly
File
"/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ipyrad/core/assembly.py",
line 27, in <module>
from ipyrad.assemble.util import *
File
"/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ipyrad/assemble/__init__.py",
line 2, in <module>
from . import demultiplex
File
"/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/ipyrad/assemble/demultiplex.py",
line 14, in <module>
import cPickle as pickle
ModuleNotFoundError: No module named 'cPickle'
i dont understand how to handle it
Thank you in an advance
On Fri, Dec 20, 2019 at 4:55 PM Greg Werner <[email protected]> wrote:
> Hi Safiqul!
>
> I’m also a MacBook Pro user, so I’ll share how my local setup works. There
> are three general options that I have found to work: conda with conda
> environments, pip with virtual environments, and docker images/containers.
>
> - Conda: I would assume you have conda installed since the readme for
> ipyrad <https://github.com/dereneaton/ipyrad> only includes installation
> instructions for conda. However, I would recommend using conda
> environments
> <https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-environments.html#>.
> This helps isolate your conda environments and helps you remain sane :-).
> - Pip: When using pip you can isolate your environments with venv
> <https://packaging.python.org/tutorials/installing-packages/#creating-virtual-environments>
> (or
> other virtual environment manager such as virtualenv
> <https://github.com/pypa/virtualenv>).
> - Docker: using docker <https://www.docker.com/products/docker-desktop> allows
> you to isolate your environment within containers. You can also combine the
> use of virtual environments within the container itself. The jupyter
> docker-stacks <https://github.com/jupyter/docker-stacks> images have lots
> of packages pre installed.
>
> Once you have your environment setup then:
>
> 1. Activate your virtual environment
> 2. Install package(s)
> 3. Launch jupyter notebook
>
> With docker, you can either build the image from scratch or download one
> of the pre built images from jupyter docker-stacks
> <https://github.com/jupyter/docker-stacks> which already have conda
> installed. Then launch your container and notebook. If things work ok, then
> you can install ipyrad using notebook magics or the included terminal. This
> makes it flexible for you to customize your environment and share it with
> others using a standard docker image regardless of their O/S.
>
>
>
> On Dec 20, 2019, at 10:21 AM, Safiqul Islam <[email protected]> wrote:
>
> Dear all
>
> I am trying to use jupyter notebook for my analysis but i could sove this
> is problem.I am a MacBook Pro user.
> I wanted import ipyrad
>
> import ipyrad as ipimport ipyrad.analysis as ipa
>
> but i could not manage,
> I am quite some of you know how to solve it, please help me thanks a lot
>
>
> <Screenshot 2019-12-20 at 16.18.00.png>
>
>
>
>
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--
Safiqul Islam
Founder & CEO, wildmentor (http://www.wildmentor.org/)
Scientific Assistant at Senckenberg Naturhistorische Sammlungen Dresden (
http://www.senckenberg.de/)
Doctoral Student (Phylogeography-Ornithology) at Ludwig-Maximilians-Universität
München (http://www.uni-muenchen.de/)
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