Cactus 2.8.3 2024-06-12

Cactus 2.8.3 is available in the following forms:

• Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.8.3
  GPU-accelerated Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.8.3-gpu
  Install instructions in README.md
• Pre-compiled Binaries Linux Tarball: cactus-bin-v2.8.3.tar.gz
  Install instructions in BIN-INSTALL.md
• Pre-compiled Binaries For Older CPU Architectures Linux Tarball: cactus-bin-legacy-v2.8.3.tar.gz
  Install instructions in BIN-INSTALL.md
• Source Tarball: cactus-v2.8.3.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.

Note: The gpu docker image was built using this patch that bumps the Ubuntu version from 20.04 to 22.04.

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.

Important note about installing on Python3.8: You may need to run python3 -m pip install backports.zoneinfo

Release Notes

This release fixes some bugs and updates to the latest Toil.

• Fix broken --restart option in cactus-graphmap
• Raise Toil job memory requirement for filter-paf-deletions
• Update to vg v1.57.0
• Update Toil to v7.0
• Fix bug where trim-outgroups job could requeset way too little memory when there are no outgroups
• Fix typo that broke cactus-maf2bigmaf on uncompressed inputs
• More robust implementation of vcfwave
• Fix bug where RED preprocessing crashed awk returned a number in scientific notation