singularity-mmseqs2

Singularity container for MMseqs2 (Many-against-Many sequence searching), a software suite for searching and clustering huge protein and nucleotide sequence sets.

Versions

Version	Directory
18.8cc5c	18.8cc5c/

Requirements

• Singularity / Apptainer
• sudo privileges (for building)

Build

cd 18.8cc5c
./build.sh

This produces singularity-mmseqs2-18.8cc5c.sif.

Usage

Direct invocation

# Run mmseqs via the container
singularity run singularity-mmseqs2-18.8cc5c.sif <command>

# Or with exec
singularity exec singularity-mmseqs2-18.8cc5c.sif mmseqs --help

Example workflow

A full example (create databases, search, convert results) is provided:

cd 18.8cc5c
./example.sh

The example creates two FASTA files, builds MMseqs2 databases, runs a search with --min-seq-id 0.3, and outputs results in BLAST tab (.m8) format.

Common commands

# Build a sequence database
singularity exec mmseqs2.sif mmseqs createdb query.fasta queryDB

# Search
singularity exec mmseqs2.sif mmseqs search queryDB targetDB resultDB tmp --min-seq-id 0.3

# Convert results to BLAST tab format
singularity exec mmseqs2.sif mmseqs convertalis queryDB targetDB resultDB results.m8

Lmod Module

A Lmod modulefile is included at 18.8cc5c/modulefile.lua. To install:

1. Copy the .sif and modulefile.lua to your modules directory (e.g., /opt/packages/mmseqs2/18.8cc5c/).
2. Load the module:

module load mmseqs2/18.8cc5c
mmseqs --help

The module sets MMSEQS2_SIF and MMSEQS2_DIR environment variables and exposes mmseqs as a shell function that delegates transparently to the container.

References

• MMseqs2 GitHub: https://github.com/soedinglab/MMseqs2
• Steinegger M & Söding J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nature Biotechnology, 2017.

---

Copyright © 2020-2026 Pittsburgh Supercomputing Center. All Rights Reserved.

The Biomedical Applications Group at the Pittsburgh Supercomputing Center in the Mellon College of Science at Carnegie Mellon University.