ComparativeGenomicsToolkit/cactus: Cactus 2.2.0 2022-08-19

Cactus 2.2.0 is available in the following forms:

• Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.2.0 GPU-accelerated Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.2.0-gpu Install instructions in README.md
• Pre-compiled Binaries Linux Tarball: cactus-bin-v2.2.0.tar.gz Install instructions in BIN-INSTALL.md
• Pre-compiled Binaries For Older CPU Architectures (no pangenome support) Linux Tarball: cactus-bin-legacy-v2.2.0.tar.gz Install instructions in BIN-INSTALL.md
• Source Tarball: cactus-v2.2.0.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 (but don't yet support the Cactus's pangenome pipeline).

Please subscribe to the cactus-announce low-volume mailing list to receive notice of Cactus release.

This release contains a major update to the "blast" phase, where chaining logic is introduced to select lastz anchors, replacing the old quality-based heuristic. It also uses 1 fewer outgroup (2 instead of 3) by default, and no longer explicitly computes self-alignments, which should result in faster runtimes.

Other changes include:

• Complete rewrite and drastic simplification of all code used to genereate lastz anchors
• PAF format now used natively throughout Cactus (replacing lastz cigars)
• Major refactor and cleanup of the "progressive" python module, removing vestiges of old Progressive Cactus repo
• Rewrite and simplifcation of the "Cactus Workflow" Python code.
• Intermediate files (project, multicactus project, experiment XML) all done away with.
• More explicit error message for "illegal instruction" signal (which commonly confused people trying to run on older CPUs)
• Fasta contig name checking and prefixing done at beginning of each tool (this should prevent cryptic halAppendSubtree errors in the pangenome pipeline)
• Update to newest SegAlign, which should fix an overflow bug that occurs when repeatmasking some data.
• Increase binary compatibility by linking with newer libxml2
• Add cactus-terra-helper tool to force-resume Terra workflows (when its own call caching fails)
• Small cleanup of cactus-preprocess interface