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patrickwest / EukRep

Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
MIT License
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Installation Error on MacOSX #19

Open ReneKat opened 2 years ago

ReneKat commented 2 years ago

Happy New Year EukRep team! I have installed EukRep onto my Mac OSX 10.14.6 using conda create -y -n eukrep -c bioconda scikit-learn==0.19.2 eukrep I cloned the EukRep git repository and added its directory to my path. I am trying to run EukRep for the first time and am getting an Import Error:

EukRep -i assembly.fa -o euk_contigs.fa --min 1000 --prokarya pro_contigs.fa

Traceback (most recent call last): File "/Users/Owl/opt/anaconda3/envs/eukrep/bin/EukRep", line 12, in import EukRep.EukRep as EukRep ImportError: No module named EukRep.EukRep

I'm hoping this is an easy fix. Thanks for your guidance! René

SilentGene commented 2 years ago

Hi @ReneKat I had the same issue and I finally sorted it out. The problem was that conda installed python2.7 by default, but the EukRep module is developed in python 3. You can solve the problem by installing python3 first before you install eukrep. The code is as below for your reference:

conda create -y -n eukrep python=3.6
conda activate eukrep
conda install -c bioconda scikit-learn==0.19.2 eukrep

However, I recommend the author solve this by assigning python version in the conda recipe, which will solve the problem fundamentally.

Cheers, Heyu

bgruening commented 2 months ago

I think we can avoid this by creating a proper conda package for EukRep.