Cactus 2.6.6 2023-08-03

Cactus 2.6.6 is available in the following forms:

• Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.6.6
  GPU-accelerated Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.6.6-gpu
  Install instructions in README.md
• Pre-compiled Binaries Linux Tarball: cactus-bin-v2.6.6.tar.gz
  Install instructions in BIN-INSTALL.md
• Pre-compiled Binaries For Older CPU Architectures Linux Tarball: cactus-bin-legacy-v2.6.6.tar.gz
  Install instructions in BIN-INSTALL.md
• Source Tarball: cactus-v2.6.6.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 fixes a compatibility problem between Cactus and the newly released vg version 1.50.0.

• Update to vg v1.50.0
• Patch hal2vg to never write reference path names of the form SAMPLE#CONTIG, as vg now fails with an exception when reading them with convert. Instead, SAMPLE#HAPLOTYPE#CONTIG is always used, even if there is no haplotype specified (in which case it's set to 0).
• Add (prototype) --haplo option to build new subsampling-compatible giraffe indexes.