Cactus 2.6.13 2023-11-15

Cactus 2.6.13 is available in the following forms:

• Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.6.13
  GPU-accelerated Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.6.13-gpu
  Install instructions in README.md
• Pre-compiled Binaries Linux Tarball: cactus-bin-v2.6.13.tar.gz
  Install instructions in BIN-INSTALL.md
• Pre-compiled Binaries For Older CPU Architectures Linux Tarball: cactus-bin-legacy-v2.6.13.tar.gz
  Install instructions in BIN-INSTALL.md
• Source Tarball: cactus-v2.6.13.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 an issue where Toil can ask for way too much memory for minigraph construction

• Cut default minigraph construction memory estimate by half
• Add --mgMemory option to override minigraph construction memory estimate no matter what
• Exit with a clear error message (instead of more cryptic crash) when user tries to run container binaries in a container
• Fix double Toil delete that seems to cause fatal error in some environments
• Fix gfaffix regular expression bug that could cause paths other than the reference to be protoected from collapse.