RE: pickle package not found

[Andrew Hess]

This is to offer some guidance for those who wish to create a conda environment for chopchop (I couldn’t comment on the original post for some reason).

I found that this recipe worked:

conda install -c anaconda biopython pandas numpy scipy argparse mysql-python scikit-learn=0.18.1

A few warnings/errors pop up when the environment is activated, but everything seems to run without any issues.

[Stephane Plaisance]

pip install pickle also fails and warns that python 2.7 is discontinued.

Are there plans to port chopchop to python3?

[Stephane Plaisance]

but this works: pip install pickle-mixin (https://stackoverflow.com/questions/48477949/not-able-to-pip-install-pickle-in-python-3-6/48477988)

[Andrew Hess]

As far as I know, pickle is installed along with python by default as part of the standard library, so you don’t need to explicitly install it (which is why the recipe I provided works).

I’m not the developer (just thought I would help with the environment because I was able to get something working), so I can’t tell you whether or not there are plans to port chopchop to python3.

[Stephane Plaisance]

Hi Andrew, Yes I know you are not responsible for this channel and I thanks you very much for your help, you allowed me install it and I am very grateful. The remark was for the developer who I hope will read it and consider the request.

Best

[Kornel Labun]

We are porting chopchop to python 3, but this is work in progress. We need to make a lot of dependencies to docker etc., but in less than half a year it should be ready.

[Kornel Labun]

I have added your conda recipe to the readme for now.