Cactus 2.9.3 2024-11-18

Cactus 2.9.3 is available in the following forms:

• Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.9.3
  GPU-accelerated Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.9.3-gpu
  Install instructions in README.md
• Pre-compiled Binaries Linux Tarball: cactus-bin-v2.9.3.tar.gz
  Install instructions in BIN-INSTALL.md
• Pre-compiled Binaries For Older CPU Architectures Linux Tarball: cactus-bin-legacy-v2.9.3.tar.gz
  Install instructions in BIN-INSTALL.md
• Source Tarball: cactus-v2.9.3.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.

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 new options to the pangenome pipeline, and hopefully improves robustness overall

• Faster path normalization (vg paths -n) for pangenomes via vg upgrade to v1.61.0
• Sanity checks added to better detect corrupted intermediate FASTA files
• Switch off abPOA's progressive mode unless input sequences have same length (otherwise sort by length)
• --lastTrain / --scoresFile options added to learn and/or use custom scoring models for multiple alignment using last-train.
• Update to latest vcflib. Also add vcflib installation command as option to BIN-INSTALL instructions
• Make --maxLen default value consistent between cactus-align --pangenome and cactus-pangenome. Previously it was 100X bigger in the former, which made it very easy to have wildly different performance between the all-at-once and step-by-step versions of the pipeline
• Fix bug where --binariesMode singularity could potentially attempt to write temporary files outside specified workDir
• Tighten disk usage estimate for tile_alignments job
• Patch mafTools to fix a bug where taffy normalization in cactus-hal2maf would crash if 1-character genome names were present in the input