Cactus 2.6.9 2023-10-20

Cactus 2.6.9 is available in the following forms:

• Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.6.9
  GPU-accelerated Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.6.9-gpu
  Install instructions in README.md
• Pre-compiled Binaries Linux Tarball: cactus-bin-v2.6.9.tar.gz
  Install instructions in BIN-INSTALL.md
• Pre-compiled Binaries For Older CPU Architectures Linux Tarball: cactus-bin-legacy-v2.6.9.tar.gz
  Install instructions in BIN-INSTALL.md
• Source Tarball: cactus-v2.6.9.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 contains some bug fixes and changes to docker image uploads

• GFAffix updated to latest release
• CI no longer pushes a docker image to quay.io for every single commit.
• CPU docker release now made locally as done for GPU
• --binariesMode docker will automatically point to release image (using GPU one as appropriate)
• --consMemory overrides hal2vg memory as well
• --defaulMemory defaults to 4Gi when using docker binaries
• SegAlign job memory specification increased to something more realistic
• --lastzMemory option added to override SegAlign memory -- highly recommended on SLURM
• chromosome (.vg / .og) outputs from pangenome pipeline will have ref paths of form GRCh38#0#chr1 instead of GRCh38#chr1 to be more consistent with full-genome indexes (and PanSN in general)