Recently I need to use rthoFinder to get more info about my gene of intersted. At first I thought it is easy, just follow the instructions on github. Things turns out I was wrong. It just shows endless error. With the help of my collegue, I realized the miniconda I installed was based on python3 but the OrthoFinder required is python2. How to switch from the default python 3 to python2?
After googling, I find out one solution good for my case. I'll explain the code here as much as I can.
First you want to make sure the opearte system has both two version python. If you type: python. It comes out Python 3.5 or whatever start with 3, it is python3. Then use quit() to quit python.
If you type: python2 , it comes out Python2.7 or whatever start with 2, it's python2. Which means your system has both the two systems.
If you type: python2 and it doesn't come out any version of python2, it means you will need to install python2 in miniconda3. Install it first.
Okay now, in your conda,you have both python2 and python3.
Then you creat a python2 enverioment by typing:
conda create --name py2 python=2.7Then you activate the environmnent by typing
conda activate py2Finally step!
install -c bioconda orthofinderGo to your Orthofinder dir and type Orthofinder it will show the help documents! Yeah!