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Releases: ComparativeGenomicsToolkit/cactus

Cactus 2.4.3 2023-03-07

07 Mar 20:04
@glennhickey glennhickey
v2.4.3
71e8c02
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Cactus 2.4.3 2023-03-07

Cactus 2.4.3 is available in the following forms:

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 patches a critical pangenome indexing bug introduced in v2.3.0, where a typo in the refactor of cactus-graphmap-join effectively caused all variation to be removed from the allele-frequency-filtered (ie .d2) graphs.

Changes

  • Fix typo in cactus-graphmap-join where minimum fragment length (default 1000) was passed as minimum depth to vg clip, overriding the correct value.
  • Introduce stub filtering in cactus-graphmap-join that cleans out all dangling nodes. Resulting graphs will have exactly two stubs (tips) per reference chromosome (just like minigraph). This can be toggled off via the removeStubs config parameter.
  • Update HAL to fix a bug in halRenameSequences
Assets 5
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Cactus 2.4.2 2023-02-14

15 Feb 00:47
@glennhickey glennhickey
v2.4.2
2d6c076
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Cactus 2.4.2 2023-02-14

Cactus 2.4.2 is available in the following forms:

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

Changes include:

  • Update HAL to fix halAppendSubtree crash in certain cases (for real this time)
  • Upgrade to Toil 5.9.2 (ditto)
Assets 5
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Cactus 2.4.1 2023-02-08

08 Feb 14:18
@glennhickey glennhickey
v2.4.1
97eddda
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Cactus 2.4.1 2023-02-08

Cactus 2.4.1 is available in the following forms:

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

Changes include:

  • Fix bug that could cause cactus-graphmap-join to crash when running vg clip
  • Upgrade to Toil 5.9.0
  • Include taffy binary with bgzip support enabled
  • Better error when trying to install on Python version < 3.7
Assets 5
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Cactus 2.4.0 2023-01-09

09 Jan 17:50
@glennhickey glennhickey
v2.4.0
47f9079
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Cactus 2.4.0 2023-01-09

Cactus 2.4.0 is available in the following forms:

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 drastically increases Cactus's default chaining parameters, resulting in much cleaner and more linear alignments.

Other changes include

  • Upgrade to Toil 5.8.0, which allows GPU counts to be assigned to jobs (which can be passed from cactus via the --gpu option). Toil only currently supports this functionality in single machine mode.
  • Fix bug introduced in v2.3.1 that broke GPU-enabled lastz preprocessing
  • Include latest vg release.
  • Include latest version of taffy (fka taf).
Assets 5
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Cactus 2.3.1 2022-12-23

23 Dec 14:57
@glennhickey glennhickey
v2.3.1
34aebb0
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Cactus 2.3.1 2022-12-23

Update (2023-01-04): GPU preprocessing is broken in this release. Please use v2.3.0 for GPU acceleration until a newer release is available.

Cactus 2.3.1 is available in the following forms:

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 bugfixes and changes that should result in cleaner alignments in pangenome mode in some cases.

  • Re-activate pangenome-specific paf filters (these were deactivated by accident back in v2.2.0, and were important in difficult regions in acrocentric chromosomes in HPRC graph).
  • Pangenome pipeline now included in legacy binaries.
  • Use mash distance (by default) to determine the minigraph construction order
  • Update HAL to fix halAppendSubtree crash in certain cases
  • Log blossom5 stderr to hopefully help debug failurs associated with it.
Assets 5
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Cactus 2.3.0 2022-11-21

22 Nov 00:09
@glennhickey glennhickey
v2.3.0
e01b445
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Cactus 2.3.0 2022-11-21

Update 2022-12-07: cactus-bin-v2.3.0.tar.gz fixed to include working vg binary. Thanks @leleory for noticing.

Cactus 2.3.0 is available in the following forms:

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 contains substantial changes to the Minigraph-Cactus pangenome pipeline, namely in cactus-graphmap-join.

  • The SAMPLE.HAPLOTYPE naming convention now only needed for non-haploid samples: you no longer need to add .0 to non-reference samples
  • All paths, including reference, are stored as W-lines in the GFA output (previously the reference was stored as a P-line)
  • XG/GBWT/GG output replaced with GBZ
  • Latest vg now shipped with Cactus (was stuck at v.1.40.0 for a while). In most cases vg version >= 1.44.0 is now required to use the output.
  • Giraffe indexing should now be more efficient
  • cactus-graphmap-join now only needs to be run once. Previously, up to 3 times was suggested. The single invocation of cactus-graphmap-join can still create up to three graphs and sets of indexes. Sensible defaults are provided to encourage users to, for example, index the filtered graph.
  • Many options from cactus-graphmap-join have been removed or moved into the config xml
  • --delFilter now enabled by default in cactus-graphmap. In addition, it is broadened to disallow any contig from inducing a deletion greater than (half) its length. (this ratio can be controlled using the delFilterQuerySizeThreshold config parameter).
  • cactus-graphmap-join will no longer ever produce a graphs with edges that aren't covered by any paths (was rare but possible before).
  • minigraph version included update to fix assertion failure bug.
  • mafTools binaries now included in Cactus.
  • Toil caching turned off by default when using the slurm batch system.

Contributors

leleory
Assets 5
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Cactus 2.2.4 2022-11-03

03 Nov 14:09
@glennhickey glennhickey
v2.2.4
b699f6b
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Cactus 2.2.4 2022-11-03

Cactus 2.2.4 is available in the following forms:

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 contains some small bugfixes in addition to improved MAF output support

  • New tool cactus-hal2maf added to speed up HAL->MAF conversion (replaces the old hal2mafMP.py from HAL), and includes TAF-based normalization and reference gaps.
  • Big documentation refactor
  • --includeRoot option added to cactus-prepare
  • Phast binaries now included in Cactus release (previously only halPhyloP was included)
  • cactus --root option regression from v2.2.0 is fixed
  • Better error-handling in case of degree-2 ancestral nodes (1-parent, 1-descendant) in input tree
  • Update HAL to version with improved memory utilization for hal2maf, halExport and halAppendSubtree, and new tool halRemoveSubtree
Assets 5
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Cactus 2.2.3 2022-10-04

04 Oct 19:04
@glennhickey glennhickey
v2.2.3
5a8c1fd
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Cactus 2.2.3 2022-10-04

Cactus 2.2.3 is available in the following forms:

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 contains yet another patch regarding the minimumBlockDegreeToCheckSupport filter option, this time in progressive alignment. It was supposed to have been toggled off entirely in v2.2.0 but instead was applied to all blocks.

  • minimumBlockDegreeToCheckSupport of <= 0 now interpreted as disabling the filter, rather than applying it to all blocks with > 0 support. Before v2.2.0 it was applied to blocks with support > 10, since v2.2.0 it was applied to blocks with support > 0, and now it is disabled.
Assets 5
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Cactus 2.2.2 2022-09-28

28 Sep 20:38
@glennhickey glennhickey
v2.2.2
6d46f24
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Cactus 2.2.2 2022-09-28

Cactus 2.2.2 is available in the following forms:

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 a critical bug in cactus-align --pangenome that was introduced in v2.2.0 and causes massive under-alignments in pangenome graphs with more than 10 or so samples. Huge thanks to @minglibio for catching this!

  • cactus-align --pangenome fixed to properly set pangenome overrides in the config.
  • gfaffix updated to fix cactus-graphmap-join crash while normalizing some types of hairpins in the graph. also, uncovered nodes left by gfaffix now filtered out before they can cause errors in deconstruct.
  • fix cactus-graphmap regression where it woudn't run with docker binaries due to directory issues.
  • cactus-minigraph now adds (non-reference) genomes in order of decreasing size by default.
  • --realTimeLogging enabled by default
  • better error message when invalid --root supplied to cactus
  • print cactus commit at the top of each log

Contributors

minglibio
Assets 5
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Cactus 2.2.1 2022-09-07

07 Sep 20:12
@glennhickey glennhickey
v2.2.1
98c9f85
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Cactus 2.2.1 2022-09-07

Cactus 2.2.1 is available in the following forms:

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 patches recent regressions in the "blast" phase:

  • Fix cactus-blast crash when using GPU on mammalian-sized genomes
  • Use tree distance (rather than 1) for determining lastz parameters for outgroups.

Other changes include:

  • Fix regression in 2.2.0 where "legacy" binary release was built with same compiler options as normal release (and therefore no more portable).
  • Make WDL output from cactus-prepare a bit cleaner. Revise Terra best practices in the documentation to be much more efficient.
  • Update to Toil 5.7.1
  • Update to minigraph 0.19
Assets 5
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