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1. Installing DUMMEST

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Harvey Chua edited this page Oct 12, 2026 · 8 revisions

You can obtain DUMMEST in one of several ways: (1) by downloading a pre-built container image or (2) by building it directly.

Basic system requirements

  • Operating System: tested on Linux
  • CPU : Intel Haswell (2013) or above, AMD Excavator (2015) or above (requires AVX2 / x86-64-v3)
  • GPU (optional, for acceleration): NVIDIA (Turing, 2018 or newer)

Option 1: Downloading a pre-built image

DUMMEST ships as a single Apptainer image containing everything you need. You do not need to install or build any of it yourself. Apptainer is a container framework for running scientific software on HPC systems (or locally).

  1. Install apptainer following the instructions provided here.

  2. Download the DUMMEST apptainer image, dummest.sif, from the GitHub releases page.

  3. Validate the installation:

apptainer exec dummest.sif dummest --help

Option 2: Building directly

Host requirements

Building from source requires a C++20 compiler and CMake, plus:

  • Python 3 with the pybedtools package (tested with 0.12.0).
  • seqkit for six-frame translation (tested with 2.3.1).
  • bedtools for extracting genomic windows (tested with 2.31.1).
  • MMseqs2 with GPU support: the custom fork with per-profile ungapped-prefilter p-values. This is bundled in the container; when building directly, it is provided by the MMseqs2 submodule (branch prefilter) that ships with the repository, and building it needs the CUDA toolkit and Rust (cargo).
  1. Clone the repository and initialize its submodules (this also fetches the bundled MMseqs2 fork):
git clone https://github.com/bioinfodlsu/dummest.git
cd dummest
git submodule update --init --recursive
  1. Install the remaining dependencies:
sudo apt install bedtools seqkit    # tested: bedtools 2.31.1, seqkit 2.3.1
pip3 install pybedtools             # tested: 0.12.0 (add --break-system-packages on Ubuntu 24.04 if needed)
  1. Build the MMseqs2 prefilter fork and add it to your PATH (drop -DENABLE_CUDA=1 for a CPU-only build):
cmake -S MMseqs2 -B build-mmseqs -DCMAKE_BUILD_TYPE=Release -DENABLE_CUDA=1
cmake --build build-mmseqs --parallel --target mmseqs
export PATH="$PWD/build-mmseqs/src:$PATH"
  1. Build DUMMEST and add its binaries to your PATH:
cmake -B build -DCMAKE_BUILD_TYPE=Release
cmake --build build --parallel
export PATH="$PWD/bin:$PATH"

You can now run dummest:

dummest profile.hmm profile.msa queryDNA.fa 8

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