We are using python2.7 and do not want to touch python3 as they interfered severely in the past that needed much work to solve. So I installed conda2 that seems working (although “source deactivate” may not seem to work somehow).
I want to install now qiime2 2018.4, and according to the instruction I should download and use qiime2-2018.4-py35-linux-conda.yml
When I read this filename I got very worried that the -py35- token in the middle refers to python3.5 that I am afraid from like hell.
Can I use this file on a linux that uses python2.7 and conda2 without mixing up all dependencies and destroying my system?
I’m not entirely sure, but I think the Conda environments are self-contained and thus while you can have two installations of Python (2 and 3) it shouldn’t interfere with your other environments. This is what I’ve been told, but I tend not to code in python.
Yes, QIIME 2 runs with Python 3.
Yes, you should be able to. If you follow the instructions to install qiime2 from within a conda environment, you will basically only download and use Python 3 from within the QIIME 2 environment. It shouldn’t change any of your defaults on your root system.
We use QIIME 2 on our lab’s cluster, which runs Python 2 and uses conda2 automatically for all other things (except when we are in the QIIME 2 environment, when it knows to look for things in the conda3 paths).
If you look at the installation steps provided by the QIIME 2 docs, you’ll see that you first download a file listing requirements for QIIME 2, and then create a new environment based on those files (but which should not change any defaults on your system). (The
qiime2-2018.4-py35-linux-conda.yml file is just a text file, so you can download this and look at it without fear of accidentally installing anything!)
Anyway, no promises that this will work straight out of the box (the real QIIME 2 devs can perhaps provide more nuance/confidence in this reply), but if you keep things within separate environments then in theory there should be no conflicts…
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.