Cactus 2.5.1 2023-04-19

Cactus 2.5.1 is available in the following forms:

• Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.5.1
  GPU-accelerated Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.5.1-gpu
  Install instructions in README.md
• Pre-compiled Binaries Linux Tarball: cactus-bin-v2.5.1.tar.gz
  Install instructions in BIN-INSTALL.md
• Pre-compiled Binaries For Older CPU Architectures Linux Tarball: cactus-bin-legacy-v2.5.1.tar.gz
  Install instructions in BIN-INSTALL.md
• Source Tarball: cactus-v2.5.1.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 mostly patches some bugs in the pangenome pipeline

• cactus-pangenome now saves PAF file in the output directory
• Ship version of vg that is patched to not make too-slow giraffe indexes for some complex graphs
• Fix bug where . characters in reference sample name could lead to strange errors at end of pipeline
• Better sample name validation for all pangenome tools to prevent confusion around .s.
• Update taffy to fix issues where --filterGapCausingDupes could lead to crashes in cactus-hal2maf
• Strip defaults of taffy commands from being specified in cactus-hal2maf -- they are now taken from taffy
• Add MHC and GRCh38-alt pangenome examples