biology/fasda-utils: Fast and simple differential analysis extras
biology/subread: Update to 2.1.0
biology/sra-tools: Update to 3.2.1
biology/py-macs3: Unbreak package build
sysutils/desktop-installer: Update to 1.1.0.6
science/csvtk: Update to 0.33.0
math/py-hmmlearn: Unbreak poudriere build
biology/py-macs3: Update to 3.0.3
biology/ncbi-blast+: Update to 2.16.0_3
biology/py-crossmap: Update to 0.7.3
biology/vsearch: Update to 2.30.0
Multiple biology ports: Replace pypi homepage with github
biology/freebayes: Update to 1.3.9
biology/tabixpp: Undeprecate and update to 1.1.2
biology/tabixpp: Update to 1.1.2
devel/intervaltree: Minimal C++ interval tree implementation
biology/vsearch: Update to 2.29.4
archivers/vbz-compression: Update to 1.0.13
sysutils/desktop-installer: Update to 1.1.0.5
sysutils/desktop-installer: Update to 1.1.0.2
sysutils/desktop-installer: Update to 1.1.0
sysutils/auto-admin: Update to 0.8.1
textproc/xml-format: Add missing dep
textproc/xml-format: Update to 0.2.0.3
sysutils/mcweject: Deprecate
sysutils/endian: Update to 1.1.6
sysutils/diskimage-tools: Update to 0.3.1.1
math/matlab-installer: Deprecate
math/matlab-installer: Deprecate
devel/roboctl: Update to 0.3.9.4
www/webbrowser: Update to 0.4.0
devel/libgamepad: Update to 0.1.2.4
biology/sra-tools: Update to 3.2.0
biology/mmseqs2: Update to 17.b804.f
science/packmol: Update to 20.15.3
devel/R-cran-optparse: Update to 1.7.5
biology/subread: Update to 2.0.8
biology/stacks: Update to 2.68
biology/py-bcbio-gff: Update to 0.7.1
biology/bbmap: Update to 39.15
biology/mmseqs2: Update to 16.747.c6
biology/ncbi-blast+: Update to 2.16.0
archivers/vbz-compression: Update to 1.0.12
archivers/streamvbyte: Update to 2.0.0
biology/bbmap: Update to 39.14
science/csvtk: Update to 0.32.0
biology/vsearch: Update to 2.29.2
biology/py-multiqc: Add missing py-natsort RUN_DEPEND
graphics/py-spectra: Add missing py-colormath RUN_DEPEND
security/hidden-lake: F2F Anonymous network based on the QB-problem
biology/gemma: Update to 0.98.5
biology/fasttree: Update to 2.1.11
biology/ucsc-userapps: Update to v474
biology/py-htseq: Update to 2.0.9
biology/vcflib: Update to 1.0.12
preseq: Not for 32-bit platforms
biology/bwa: Update to 0.7.18
graphics/py-plotly: Fix mangled pkg-descr
biology/preseq: Predict yield of distinct reads from a genomic library
biology/py-multiqc: Update to 1.25.2
sysutils/devd-mount: CONFLICTS -> CONFLICTS_INSTALL
filesystems/automount: Add CONFLICTS_INSTALL=devd-mount
sysutils/devd-mount: Add CONFLICTS=automount
deskutils/freebsd-update-notify: Update to 0.1.1.11
biology/sra-tools: Update to 3.1.1
deskutils/freebsd-update-notify: Update to 0.1.1.8
deskutils/freebsd-update-notify: Update to 0.1.1.7
biology/sra-tools: Quick fix to unbreak build
biology/fastp: Update to 0.24.0
biology/py-multiqc: Update to 1.25.1
graphics/py-plotly: Update to 5.24.1
sysutils/devd-mount: Update to 0.2.0
deskutils/qmediamanager: Update to 0.1.2
biology/biostar-tools: Update to 2.0
biology/ucsc-userapps: Change license to MIT
biology/ucsc-userapps: Update to 472
science/csvtk: Update to 0.31.0
math/py-hmmlearn: Update to 0.3.3
deskutils/coregarage: Update to 4.5.0
x11/coreterminal: Update to 4.5.0
deskutils/libcprime: Update to 4.5.0
biology/vsearch: Update to 2.29.1
sysutils/auto-admin: Update to 0.8.0.50
sysutils/auto-admin: Update to 0.8.0.50
biology/mca-calling: Core tools for mCA event calling
biology/vsearch: Update to 2.29.0
biology/trimadap: Update to 0.1.4
I tested on aarch64 using SIMDE. See , and let me know if it works on arm7.
I don't think it's a good idea to add a new port that's basically a small fraction of an existing, well-supported port. Redoing the patches may be a drag, but it would benefit a lot of users by supporting other platforms, and avoid leading future developers away from a better solution by example. Using SIMDE also allows ONLY_FOR_ARCHS to be removed entirely, simplifying the port. The changes needed for SIMDE are similar to what you did. Just replace emmintrin.h with something like simde/x86/sse2.h. The conversion from sse2neon to SIMDE should be easy.
I think SIMDE will do the same thing for neon, while at the same time supporting a variety of other architectures with no additional patching. I've used it successfully with aarch64, powerpc64, and riscv. Probably worth a look. Check out biology/bwa, biology/bowtie2, etc.
Did you consider using devel/simde? That's usually how I get around this sort of issue.
Did you consider using devel/simde? That's usually how I get around this sort of issue.
biology/bcftools: Update to 1.21
biology/bcf-score: Update to 1.20
biology/bio-mocha: Update to 1.20
biology/samtools: Update to 1.21
biology/htslib: Update to 1.21
biology/kallisto: Update to 0.51.1,1