Installation

Installation Guide

PMAT2 version 2.2.0 provides native binary execution on Linux x86_64 without requiring external container runtimes, as well as a prebuilt standalone container for containerized environments.

System Requirements

• Operating System: Linux x86_64 (CentOS 7+, Rocky Linux 8/9, Ubuntu 18.04+, Debian 10+).
• BLASTn > 2.10.0: Must be installed in PATH (already included if using PMAT_v2.2.0.sif).
• Canu > v2.0 or NextDenovo: Required only if performing raw ONT or CLR sequencing read error correction.
• zlib: Required only if you intend to recompile from C source code.

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Method 1: Download Release Archive

wget https://github.com/aiPGAB/PMAT2/archive/refs/tags/v2.2.0.tar.gz
tar -zxvf v2.2.0.tar.gz
cd PMAT2-2.2.0
./PMAT --help

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Method 2: Clone from GitHub

git clone --depth 1 https://github.com/aiPGAB/PMAT2.git
cd PMAT2
./PMAT --help

(Optional: If you modify the C source code, simply run make clean && make to recompile.)

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Method 3: Standalone SIF Container (Apptainer / Singularity)

For users who prefer a completely self-contained environment without configuring BLASTn on the host:

# Download the SIF image from GitHub Releases
wget https://github.com/aiPGAB/PMAT2/releases/download/v2.2.0/PMAT_v2.2.0.sif
chmod +x PMAT_v2.2.0.sif

# Execute directly
./PMAT_v2.2.0.sif autoMito --help

# Or run via apptainer
apptainer exec PMAT_v2.2.0.sif PMAT autoMito --help

Storage Mounts for Containers

When running with Apptainer, if your input sequencing data or output directory is located on non-home partitions (such as /pub, /data, or /scratch), pass -B /path to bind the storage:

apptainer exec -B /pub PMAT_v2.2.0.sif PMAT autoMito -i /pub/data.fa -o /pub/out ...