Cactus 2.6.10 2023-10-30

Cactus 2.6.10 is available in the following forms:

• Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.6.10
  GPU-accelerated Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.6.10-gpu
  Install instructions in README.md
• Pre-compiled Binaries Linux Tarball: cactus-bin-v2.6.10.tar.gz
  Install instructions in BIN-INSTALL.md
• Pre-compiled Binaries For Older CPU Architectures Linux Tarball: cactus-bin-legacy-v2.6.10.tar.gz
  Install instructions in BIN-INSTALL.md
• Source Tarball: cactus-v2.6.10.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 contains bug fixes for MAF export and the pangenome pipeline

• Patch taffy to fix bug where sometimes length fields in output MAF can be wrong when using cactus-hal2maf --filterGapCausingDupes
• Fix regression in cactus-graphmap-split / cactus-pangenome so that small poorly aligned reference contigs (like some tiny unplaced GRCh38 contigs) do not get unintentionally filtered out. These contigs do not help the graph in any way, but the tool should do what it says and make a component for every single reference contig no matter what, which it is now fixed to do.
• Cactus will now terminate with a clear error message if any other --batchSystem than single_machine is attempted from inside a docker container.
• Mash distance order into minigraph construction fixed so that haplotypes from the same sample are always added contiguously in the presence of ties.
• CI fixed to run all hal tests, and not just a subset.
• pip install wheel added to installation instructions, as apparently that's needed to install Cactus with some (newer?) Pythons.