Micromamba is a lightweight Conda-compatible package manager that lets you create reproducible software environments without needing admin rights.

On the NBI HPC, you should create and modify environments only on the software node (compilation and downloads are allowed there).
Compute jobs should use environments that are already created.

Create an environment

# Create a test environment (you MUST be in the software node!)
micromamba create -n env1 samtools=1.18 minimap2 seqfu

💡 We enabled the conda-forge and bioconda channels via configuration

Some basic commands

To list all the environments available in our installation:

micromamba env list

To activate one environment (by name):

# Activate the base environment
micromamba activate base

Running a command from an environment:

# Simply run a command without activating
micromamba run -n env1 seqfu version

# or activate first 
micromamba activate env1
seqfu version

Create an environment from a YAML file

If you want an environment that is easy to share and reproduce, use a YAML file.

Example environment.yml:

name: env1
channels:
  - conda-forge
  - bioconda
dependencies:
  - samtools=1.18
  - minimap2
  - seqfu

Create it:

micromamba env create -f environment.yml

💡 You can export an environment with micromamba env export and save it as YAML file.

Install, update, and remove packages

Install a new package into an existing environment:

micromamba install -n env1 fastp

Update a package:

micromamba update -n env1 samtools

Remove a package:

micromamba remove -n env1 fastp

Remove an environment

micromamba env remove -n env1

Where are environments stored?

You can check where micromamba stores environments with:

micromamba info

On HPC systems, environments are usually stored under your home directory (or another user-writable location). If you want to keep environments in a dedicated folder (recommended), you can set:

export MAMBA_ROOT_PREFIX=$HOME/micromamba

(You can add this to your ~/.bashrc if your site policy allows it.)

Using micromamba inside an sbatch job

You typically do not want to run micromamba create inside a job. Instead, create the environment once on the software node, then use it in jobs.

Example sbatch script:

#!/usr/bin/env bash
#SBATCH --job-name=mm_env_test
#SBATCH --partition=qib-short
#SBATCH --time=00:10:00
#SBATCH --cpus-per-task=1
#SBATCH --mem=1G
#SBATCH --output=slurm-%j.out

set -euo pipefail

# Option A: run without activating (clean and safe)
micromamba run -n env1 seqfu version
micromamba run -n env1 samtools --version
micromamba run -n env1 minimap2 --version

Common troubleshooting

micromamba: command not found

You may need to load it via modules (if available) or ensure it is in your PATH.

Try:

which micromamba

Environment activates but tools are missing

Check you are using the correct environment:

micromamba env list
micromamba list -n env1