Cactus 2.4.0 2023-01-09

Cactus 2.4.0 is available in the following forms:

• Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.4.0
  GPU-accelerated Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.4.0-gpu
  Install instructions in README.md
• Pre-compiled Binaries Linux Tarball: cactus-bin-v2.4.0.tar.gz
  Install instructions in BIN-INSTALL.md
• Pre-compiled Binaries For Older CPU Architectures Linux Tarball: cactus-bin-legacy-v2.4.0.tar.gz
  Install instructions in BIN-INSTALL.md
• Source Tarball: cactus-v2.4.0.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).

Please subscribe to the cactus-announce low-volume mailing list to receive notice of Cactus release.

Release Notes

This release drastically increases Cactus's default chaining parameters, resulting in much cleaner and more linear alignments.

Other changes include

• Upgrade to Toil 5.8.0, which allows GPU counts to be assigned to jobs (which can be passed from cactus via the --gpu option). Toil only currently supports this functionality in single machine mode.
• Fix bug introduced in v2.3.1 that broke GPU-enabled lastz preprocessing
• Include latest vg release.
• Include latest version of taffy (fka taf).