installing Qiime2 with mamba

Technical Support
, ,
1

I tried to install qiime2-2021.11-py38-linux-conda.yml with mamba and got this error:

mamba env create -n qiime2-2021.11 --file qiime2-2021.11-py38-linux-conda.yml

...

Encountered problems while solving.
Problem: nothing provides __glibc >=2.17,<3.0.a0 needed by nodejs-16.12.0-h73e1104_0
Problem: nothing provides __glibc >=2.17,<3.0.a0 needed by nodejs-16.12.0-h73e1104_0

I do not get this error with conda. :snail:

The mamba installer is much faster than conda's and is the default in snakemake. Any advice about why this is failing would be very helpful!

2

In my experience, such an error occurs due to dependency mismatch caused by installing apps from wrong channels in conda.
Try to add bioconda and conda-forge to default channels via:

conda config --add channels bioconda
conda config --add channels conda-forge

OR

add a channel specification in qiime2-2021.11-py38-linux-conda.yml:

channels:
- defaults
- conda-forge
- bioconda

Tested QIIME2 2021.11 installation 5h ago on a fresh VM via mamba. All worked smoothly by me without need to modify anything.

3

Thanks for the advice!

Those channels are already at the top of the .yml file:

(snakemake) [cbrislawn@master envs]$ head qiime2-2021.11-py38-linux-conda.yml 
channels:
  - qiime2/label/r2021.11
  - conda-forge
  - bioconda
  - defaults
dependencies:

Very interesting!

Here's my software versions. I wonder if the online database changed earlier today and we are the first to notice...

(base) [cbrislawn@master envs]$ mamba --version
mamba 0.7.5
conda 4.11.0
4

Okay, now I see.
You have the wrong version of mamba :slight_smile:
0.7.5 is actually older and it doesn't respect channels in .yml
The latest release is 0.19.1. https://anaconda.org/conda-forge/mamba
They underwent some reversioning IDK.

My stack:

mamba 0.19.1
conda 4.11.0
5

That did it!

Thank you for your help, Valentyn.