3.2.1 2026-05-20

Cactus 3.2.1 is available in the following forms:

• Docker Image: quay.io/comparative-genomics-toolkit/cactus:v3.2.1
  GPU-accelerated Docker Image: quay.io/comparative-genomics-toolkit/cactus:v3.2.1-gpu
  Install instructions in README.md
• Pre-compiled Binaries Linux Tarball: cactus-bin-v3.2.1.tar.gz
  Install instructions in BIN-INSTALL.md
• Pre-compiled Binaries For Older CPU Architectures Linux Tarball: cactus-bin-legacy-v3.2.1.tar.gz
  Install instructions in BIN-INSTALL.md
• Source Tarball: cactus-v3.2.1.tar.gz
  Install instructions in README.md

WARNING: do not use the github automatically generated source files (Source code (zip) or Source code (tar.gz)), these are not correct.

The Docker images and binaries linked above are built using AVX2 extensions, and require a CPU that supports them, except the "Pre-compiled Binaries For Older CPU Architectures" which should be compatible with any 64-bit architecture (and, since version 2.3.1, support Cactus's pangenome pipeline).

Release Notes

This release patches a critical regression from 3.2.0 that broke gpu support in docker

• Fix --gref option name incompatibility between cactus / vg; add --grefL
• Fix KegAlign bashlex error by using a slightly older KegAlign commit (same used in previous cactus release)
• Update to Toil 9.4.1