Cactus 2.6.5 2023-07-27

Cactus 2.6.5 is available in the following forms:

• Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.6.5
  GPU-accelerated Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.6.5-gpu
  Install instructions in README.md
• Pre-compiled Binaries Linux Tarball: cactus-bin-v2.6.5.tar.gz
  Install instructions in BIN-INSTALL.md
• Pre-compiled Binaries For Older CPU Architectures Linux Tarball: cactus-bin-legacy-v2.6.5.tar.gz
  Install instructions in BIN-INSTALL.md
• Source Tarball: cactus-v2.6.5.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 patches a Toil bug that broke GPU support on single-machine.

• Update to Toil v5.12, which fixes issue where trying to use GPUs on single machine batch systems would lead to a crash
• Make cactus more robust to numeric and duplicate internal node labels on input tree (ie ignore them instead of crashing with a cryptic scheduling error)
• Fix hal2chains --targetGenomes option.