Snakemake Global Environment Container

Question

[meetmet]

Hi everyone,

I’m currently working with Singularity containers for a bioinformatics project and using Snakemake to manage workflows. My goal is to make sure that my Conda environment is created within the Singularity container (which includes Miniconda3), but I’m running into an issue where it seems like the Conda environment is still being created on my local machine instead.

Here are the logs I’m seeing:

Activating singularity image /data/SaMD/.snakemake/singularity/d9...simg
Activating conda environment: .snakemake/conda/49a724..   

Docker Image:         "docker://continuumio/miniconda3:25.1.1-2"

How can I check that the conda env is created within the container?

Thanks for your futur help.

Ps: I declare the global env. container in the Snakefile as:

container: "docker://continuumio/miniconda3:25.1.1-2"

[DBScan]

How are you running snakemake?

[meetmet]

Hello,

I run snakemake from the main directory of the workflow:

snakemake --profile workflow/profile --configfile .test/config/config.yaml

The profile file content:

latency-wait: 30
scheduler: greedy
use-conda: true
conda-cleanup-pkgs: cache
use-singularity: true
printshellcmds: true
show-failed-logs: true
restart-times: 1  
jobs: 16
cores: 16
local-cores: 1
max-jobs-per-second: 5
max-status-checks-per-second: 10
rerun-incomplete: true
rerun-triggers: mtime
default-resources:
  - mem_mb=4000 

[DBScan]

You can try to add software-deployment-method: conda singularity to you profile, this should work accordin to https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#ad-hoc-combination-of-conda-package-management-with-containers

[meetmet]

Many thanks!

I completely missed this option.

Cheers.