Cactus 2.7.1 2024-01-19

Cactus 2.7.1 is available in the following forms:

• Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.7.1
  GPU-accelerated Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.7.1-gpu
  Install instructions in README.md
• Pre-compiled Binaries Linux Tarball: cactus-bin-v2.7.1.tar.gz
  Install instructions in BIN-INSTALL.md
• Pre-compiled Binaries For Older CPU Architectures Linux Tarball: cactus-bin-legacy-v2.7.1.tar.gz
  Install instructions in BIN-INSTALL.md
• Source Tarball: cactus-v2.7.1.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).

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

Release Notes

This release adds some options to tune outgroup selection, as well as updates many included dependencies and tools

• Add --chromInfo option to specify sex chromosomes of input genomes, in order to make sure outgroups are selected accordingly
• Add --maxOutgroups option so that the number of outgroups can be toggled via the command line (previously required using a modified configuration file).
• Update to Toil 6.0.0
• Update to vg 1.54.0
• Update to odgi 0.8.4
• Update to latest taffy (fixing bug in paf export)
• Update to abPOA 1.5.1
• Fix Dockerfile so that Phast binaries are included
• --indexMemory now acts as upper limit on chromosome-level jobs.