Cactus 2.0.5 2022-01-25

Cactus 2.0.5 is available in the following forms:

• Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.0.5
  GPU-accelerated Docker Image: quay.io/comparative-genomics-toolkit/cactus:v2.0.5-gpu
  Install instructions in README.md
• Pre-compiled Binaries Linux Tarball: cactus-bin-v2.0.5.tar.gz
  Install instructions in BIN-INSTALL.md
• Pre-compiled Binaries For Older CPU Architectures (no pangenome support) Linux Tarball: cactus-bin-legacy-v2.0.5.tar.gz
  Install instructions in BIN-INSTALL.md
• Source Tarball: cactus-v2.0.5.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.

Release notes

This release fixes fixes a major (though rare) bug where the reference phase could take forever on some inputs. It includes a newer version of lastz which seems to fix some crashes as well.

• Debug symbols no longer stripped from cactus_consolidated binary in Release.
• Update to Toil 3.5.6
• Update examples to use Python 3.8 specifically (was previously just python3, but this is often python3.6, support for which was dropped in Toil 3.5.6)
• cactus-prepare WDL output can now batch up hal_append_subtree jobs
• Fix bug where "reference" phase within cactus_consolidated could take ages on some input
• Fix bug where --realTimeLogging flag would cause infinite loop after cactus_consolidated within some Docker invocations.
• Upgrade to more recent version of lastz