v2026.8.5
Lungfish 2026.8.5
Channel: Stable
Previous versioned release: v2026.8.4
Stable baseline: v2026.8.4
Dependency set: 2026.2
Lungfish 2026.8.5 supersedes the first Stable CalVer build after its automatic
release board exposed a mismatch in the MEGAHIT conformance test. The shipped
assembly pipeline was already using its supported Apple Silicon command, but
the test bypassed that command builder and invoked raw MEGAHIT without
--no-hw-accel, selecting an accelerated core that aborted on the CI host.
This release contains no scientific workflow, parser, storage, database, or
dependency-pin change from 2026.8.4. It rebuilds the Stable app from the
corrected validation source, with a new version, build number, signature,
notarization record, DMG, and Sparkle item.
Included preview releases
None. No Preview release falls between Stable v2026.8.4 and this Stable
replacement.
Release validation correction
- The MEGAHIT conformance test now constructs its invocation through
ManagedAssemblyPipeline.buildCommand, the same path used by the shipped
application. - On Apple Silicon the test asserts the production safeguards explicitly:
--no-hw-accelis present and the requested four threads are capped to two. - The test executes that production command and still requires successful
assembly, a non-emptyfinal.contigs.fa, normalized output, and recorded
command provenance.
The 2026.8.4 Stable artifact passed its Fast gate and Build/smoke job; the
Toolset conformance job failed only at the obsolete raw test invocation.
2026.8.5 is issued so the immutable release tag, shipped source, and automatic
Stable validation board all describe the same verified state.
Reproducibility and provenance
Dependency set 2026.2 and every scientific tool, pipeline, database, bootstrap,
and SwiftPM pin remain unchanged. Scientific operations continue to record the
executed tool and version, exact arguments and resolved defaults, runtime
identity, input and output paths, checksums, sizes, exit status, wall time, and
useful diagnostics. The MEGAHIT conformance test now verifies the production
command line that feeds that provenance instead of maintaining a divergent
hand-written command.
Platform and release infrastructure
This is a fresh Stable-channel build. It is displayed as Lungfish Genome
Explorer (short name Lungfish), reports release channel stable, and
polls sparkle-stable/appcast-stable.xml. It does not relabel or reuse the
2026.8.4 app or DMG.
Dependency versions
The following tables reproduce every current version identity in the bundled
dependency manifest and Package.resolved. Conda identities include their
exact channel, package version, and build string.
Core managed tools
| Manifest id | Exact package identity |
|---|---|
nextflow |
bioconda::nextflow=26.04.6=h2a3209d_1 |
snakemake |
bioconda::snakemake=9.25.2=hdfd78af_0 |
bbtools |
bioconda::bbmap=40.02=he046917_0 |
fastp |
bioconda::fastp=1.3.6=ha1d0559_0 |
deacon |
bioconda::deacon=0.16.0=h314a369_0 |
samtools |
bioconda::samtools=1.24=h36b3a25_1 |
bcftools |
bioconda::bcftools=1.24=h6bd33b9_2 |
htslib |
bioconda::htslib=1.24=hd3c6ec9_0 |
seqkit |
bioconda::seqkit=2.13.0=hd5f1084_0 |
cutadapt |
bioconda::cutadapt=5.2=py313hf513372_2 |
trim_galore |
bioconda::trim-galore=2.3.0=h48b4a6d_0 |
vsearch |
bioconda::vsearch=2.31.0=h0448ff9_0 |
pigz |
conda-forge::pigz=2.8=hfab5511_2 |
sra-tools |
bioconda::sra-tools=3.4.1=h4675bf2_1 |
ucsc-bedgraphtobigwig |
bioconda::ucsc-bedgraphtobigwig=482=h1643cc5_0 |
pysam |
bioconda::pysam=0.24.0=py310hf7cbfa5_1 |
openpyxl |
conda-forge::openpyxl=3.1.5=py312h2a925e6_3 |
Plugin-pack tools
| Pack | Manifest id | Exact package identity |
|---|---|---|
| Read Mapping | minimap2 |
bioconda::minimap2=2.31=h6bd33b9_0 |
| Read Mapping | bwa-mem2 |
bioconda::bwa-mem2=2.3=hda5e58c_0 |
| Read Mapping | bowtie2 |
bioconda::bowtie2=2.5.5=h9e91881_0 |
| Full-Length MHC Genotyping | savont |
bioconda::savont=0.6.3=ha819e4a_0 |
| Full-Length MHC Genotyping | blast |
bioconda::blast=2.16.0=hb260f6e_5 |
| Variant Calling | lofreq |
bioconda::lofreq=2.1.5=py310h9cf5bfa_16 |
| Variant Calling | ivar |
bioconda::ivar=1.4.4=hda5e58c_0 |
| Variant Calling | medaka |
bioconda::medaka=2.2.2=py312h3bb865a_0 |
| Variant Calling | clair3 |
bioconda::clair3=2.0.2=py311h9aa1f4a_0 |
| GATK Core | gatk4 |
bioconda::gatk4=4.6.2.0=py310hdfd78af_1 |
| Phasing | whatshap |
bioconda::whatshap=2.3=py311h1457a19_3 |
| Assembly | spades |
bioconda::spades=4.3.0=hd468e49_1 |
| Assembly | megahit |
bioconda::megahit=1.2.9=h96a01ab_8 |
| Assembly | skesa |
bioconda::skesa=2.5.1=hda5e58c_3 |
| Assembly | flye |
bioconda::flye=2.9.6=py310hba4535a_1 |
| Assembly | hifiasm |
bioconda::hifiasm=0.25.0=h697fd72_0 |
| Multiple Sequence Alignment | mafft |
conda-forge::mafft=7.526=h99b78c6_0 |
| Phylogenetics | iqtree |
bioconda::iqtree=3.1.3=h6cc7423_0 |
| Metagenomics | kraken2 |
bioconda::kraken2=2.17.1=pl5321h158e17b_0 |
| Metagenomics | bracken |
compatibility pin bioconda::bracken=1.0.0=1; fresh installs use source overlay 3.1 with Python 3.11.13, cxx-compiler 1.9.0, and llvm-openmp 21.1.8 |
| Metagenomics | esviritu |
bioconda::esviritu=1.3.3=pyhdfd78af_0 |
| Metagenomics | ribodetector |
bioconda::ribodetector=0.3.3=pyhdfd78af_0 |
| Wastewater Surveillance | freyja |
bioconda::freyja=2.0.3=pyhdfd78af_0 |
Pipelines
| Manifest id | Release | Immutable revision |
|---|---|---|
taxtriage |
v3.3.8 |
e10bfebda32a62711f38a4e23ab03b61725a9675 |
nf-core-viralrecon |
3.0.0 |
3.0.0 |
Databases and managed data
| Manifest id | Current identity |
|---|---|
kraken2-standard |
20260626 |
kraken2-standard-8 |
20260626 |
kraken2-standard-16 |
20260626 |
kraken2-pluspf |
20260626 |
kraken2-pluspf-8 |
20260626 |
kraken2-pluspf-16 |
20260626 |
kraken2-viral |
20260626 |
kraken2-minus-b |
20260626 |
kraken2-eupathdb46 |
20230407 |
esviritu-viral-v3 |
v3.2.4 |
ncbi-taxonomy |
2025-03 |
kraken2-special-silva |
kraken2-special-v1 |
kraken2-special-greengenes |
kraken2-special-v1 |
human-scrubber |
20260706v2 |
deacon-panhuman |
panhuman-1 |
deacon-ribokmers |
bbmap-ribokmers-k31w15 |
The bootstrap identity is micromamba 2.9.0-0; its Apple Silicon payload is
checksum-verified before use.
SwiftPM resolved packages
| Package identity | Version | Revision |
|---|---|---|
async-http-client |
1.36.0 |
9544287b9416c0bc71e58b9f3aead8dd14b16103 |
containerization |
0.24.5 |
c3fe889a2f739ee4a9b0faccedd9f36f3862dc29 |
grpc-swift |
1.27.5 |
6a8927df5a91710b414caba4f8a088dead4633db |
sparkle |
2.9.6 |
ac2def288cbff5cfc7df3ffef6abdf45b72bcb0a |
swift-algorithms |
1.2.1 |
87e50f483c54e6efd60e885f7f5aa946cee68023 |
swift-argument-parser |
1.8.2 |
6a52f3251125d74daf04fcbd5e6f08a75d074382 |
swift-asn1 |
1.7.1 |
a9a5efd40eaf558a2bcd48d64b1d1646be686008 |
swift-async-algorithms |
1.1.5 |
3da39bbc4e687d4192af7c9cf4eab805745a0b9c |
swift-atomics |
1.3.1 |
0442cb5a3f98ab802acb777929fdb446bda11a34 |
swift-certificates |
1.19.4 |
449dbbecd0f31e82b510ada227ca152caa8b5e98 |
swift-collections |
1.6.0 |
a0cb0954ecb21e4e31b0070e6ed5674e8556685a |
swift-configuration |
1.2.0 |
be76c4ad929eb6c4bcaf3351799f2adf9e6848a9 |
swift-crypto |
3.15.1 |
95ba0316a9b733e92bb6b071255ff46263bbe7dc |
swift-distributed-tracing |
1.4.1 |
dc4030184203ffafbb2ec614352487235d747fe0 |
swift-http-structured-headers |
1.7.0 |
933538faa42c432d385f02e07df0ace7c5ecfc47 |
swift-http-types |
1.6.0 |
db774a277f60063a32d854f2980299caf06da041 |
swift-log |
1.15.0 |
3ffafb9722d5d918c614feb496c8789a3b59d222 |
swift-nio |
2.101.3 |
0b18836bd8b0162e7e17a995a3fbee20ed8f3b2b |
swift-nio-extras |
1.34.3 |
88a51340f59cf181ebde888bd1b749296b3ec029 |
swift-nio-http2 |
1.45.0 |
45bdf670248be5f16ec0340e125dca285536f0fb |
swift-nio-ssl |
2.37.2 |
d930168b86f46ca51a4bc09c5ca45c1833db8067 |
swift-nio-transport-services |
1.28.0 |
67787bb645a5e67d2edcdfbe48a216cc549222d5 |
swift-numerics |
1.1.1 |
0c0290ff6b24942dadb83a929ffaaa1481df04a2 |
swift-protobuf |
1.35.0 |
9bbb079b69af9d66470ced85461bf13bb40becac |
swift-service-context |
1.3.0 |
d0997351b0c7779017f88e7a93bc30a1878d7f29 |
swift-service-lifecycle |
2.12.0 |
7f9326b0326ff86e3646295ea6e891f68c471c5e |
swift-system |
1.8.1 |
869129b7bf4ecc57b97d0193ad29690ca2134750 |
zstd |
1.5.7 |
f8745da6ff1ad1e7bab384bd1f9d742439278e99 |
Known issues and compatibility notes
- Preview and Stable cannot be installed side by side; install the desired
channel's DMG to switch the one shared application installation. - The 20260626 Kraken2 indexes display species-level taxid 3418604 as
Betacoronavirus pandemicum. Classification identifiers are unchanged, but
searches or notes relying on the former SARS-CoV-2 display name should be
checked. - The Apple Silicon bioconda Bracken compatibility package has no real driver
and does not support domain-level profiling through its synthesized
launcher. Fresh installs receive the managed Bracken 3.1 source build;
existing working environments are preserved. bioconda::bwa-mem2=2.3=hda5e58c_0self-reports 2.2.1 because of an upstream
packaging defect. Lungfish verifies that pin from conda package metadata.