I'm trying to install the latest version of Qiime2 as a user on an HPC (I don't have write permissions to base conda to update it or run a clean install, which seems to fix this issue for others having similar conda problems). It's all fine on my local machine, which is running linux - just need the compute.
When trying to install qiime2 in a new environment, as outlined in the tutorials - I get hundreds of package conflicts and conda spends 12+ hours 'solving environment'. This results in a long list of dependency issues and eventual failure.
To get around this, I've created a new qiime2 environment, then installed qiime 2 like this:
conda create -n qiime2-2023.5
conda activate qiime2-2023.5
conda install -c "qiime2/label/r2023.5" qiime2
This seems to work fine - and the new environment's folder hierarchy is populated.
But, it doesn't install all of the dependencies from the .yml file.
Also, trying to use qiime commands results in the following:
(qiime2-2023.5) [USER@p2-log-1 qiime2-2023.5] qiime
-bash: qiime: command not found
Have also tried updating the existing environment with the .yml file using:
conda env update --file qiime2-2023.5-py38-linux-conda.yml
Which results in similar outcomes with 48h waits for conda to solve the environment and fail due to dependencies.
I've tried everything on the conda side here, including changing channel priority flexible/strict
Is there an easy way to install qiime without the .yml (using conda install seems to work okay), or another way around this? I'm at the point where I'm about to manually run through the .yml and install each dependency manually, or ask the admin to clean install miniconda/mamba, but thought I'd better check I've not missed something obvious here.
Here is my conda info:
active environment : qiime2-2023.5
active env location : /hpcfs/users/$USER/myconda/envs/qiime2-2023.5
shell level : 2
user config file : /home/$USER/.condarc
populated config files : /home/$USER/.condarc
conda version : 4.8.3
conda-build version : 3.18.11
python version : 3.8.3.final.0
virtual packages : __cuda=11.6
base environment : /apps/skl/software/Anaconda3/2020.07 (read only)
channel URLs : conda-forge/linux-64
package cache : /hpcfs/users/$USER/myconda/pkgs
envs directories : /hpcfs/users/$USER/myconda/envs
platform : linux-64
user-agent : conda/4.8.3 requests/2.24.0 CPython/3.8.3 Linux/4.18.0-305.el8.x86_64 rhel/8.4 glibc/2.28
UID:GID : 1667276:1667276
netrc file : None
offline mode : False