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jwb (jwb@freebsd.org)
Scientific computing instructor, bioinformatics consultant

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User Details

User Since
Nov 27 2017, 4:37 PM (377 w, 2 d)

Instructor for Research Computing, etc. at the University of Wisconsin -- Milwaukee

Recent Activity

Yesterday

jwb committed R11:bac90e855c13: biology/freebayes: Update to 1.3.9 (authored by jwb).
biology/freebayes: Update to 1.3.9
Tue, Feb 18, 8:47 PM
jwb committed R11:813f71aa155a: biology/tabixpp: Undeprecate and update to 1.1.2 (authored by jwb).
biology/tabixpp: Undeprecate and update to 1.1.2
Tue, Feb 18, 3:40 PM
jwb committed R11:38e86db59cdc: biology/tabixpp: Update to 1.1.2 (authored by jwb).
biology/tabixpp: Update to 1.1.2
Tue, Feb 18, 3:40 PM
jwb committed R11:03b4820d4c5b: devel/intervaltree: Minimal C++ interval tree implementation (authored by jwb).
devel/intervaltree: Minimal C++ interval tree implementation
Tue, Feb 18, 2:57 PM

Sun, Feb 16

jwb committed R11:4bbc35807790: biology/vsearch: Update to 2.29.4 (authored by jwb).
biology/vsearch: Update to 2.29.4
Sun, Feb 16, 2:21 PM
jwb committed R11:ef08ef1262c3: archivers/vbz-compression: Update to 1.0.13 (authored by jwb).
archivers/vbz-compression: Update to 1.0.13
Sun, Feb 16, 1:18 PM

Wed, Feb 12

jwb committed R11:ac235c50dc8f: sysutils/desktop-installer: Update to 1.1.0.5 (authored by jwb).
sysutils/desktop-installer: Update to 1.1.0.5
Wed, Feb 12, 7:24 PM

Sat, Feb 8

jwb committed R11:f0a998aad6e9: sysutils/desktop-installer: Update to 1.1.0.2 (authored by jwb).
sysutils/desktop-installer: Update to 1.1.0.2
Sat, Feb 8, 5:59 PM

Tue, Feb 4

jwb committed R11:222db315a10a: sysutils/desktop-installer: Update to 1.1.0 (authored by jwb).
sysutils/desktop-installer: Update to 1.1.0
Tue, Feb 4, 4:05 PM
jwb committed R11:fa1e2038c23b: sysutils/auto-admin: Update to 0.8.1 (authored by jwb).
sysutils/auto-admin: Update to 0.8.1
Tue, Feb 4, 4:05 PM
jwb committed R11:be795d728897: textproc/xml-format: Add missing dep (authored by jwb).
textproc/xml-format: Add missing dep
Tue, Feb 4, 12:49 PM

Mon, Feb 3

jwb committed R11:d426cea9b31c: textproc/xml-format: Update to 0.2.0.3 (authored by jwb).
textproc/xml-format: Update to 0.2.0.3
Mon, Feb 3, 11:17 PM
jwb committed R11:aa76d692b293: sysutils/mcweject: Deprecate (authored by jwb).
sysutils/mcweject: Deprecate
Mon, Feb 3, 11:10 PM
jwb committed R11:4c7ab59d2705: sysutils/endian: Update to 1.1.6 (authored by jwb).
sysutils/endian: Update to 1.1.6
Mon, Feb 3, 11:08 PM
jwb committed R11:97b7e676be66: sysutils/diskimage-tools: Update to 0.3.1.1 (authored by jwb).
sysutils/diskimage-tools: Update to 0.3.1.1
Mon, Feb 3, 10:26 PM
jwb committed R11:10a5ec03125f: math/matlab-installer: Deprecate (authored by jwb).
math/matlab-installer: Deprecate
Mon, Feb 3, 10:08 PM
jwb committed R11:4a351aa5583d: math/matlab-installer: Deprecate (authored by jwb).
math/matlab-installer: Deprecate
Mon, Feb 3, 9:27 PM
jwb committed R11:379a571b580c: devel/roboctl: Update to 0.3.9.4 (authored by jwb).
devel/roboctl: Update to 0.3.9.4
Mon, Feb 3, 4:45 PM
jwb committed R11:d6270774dbd2: www/webbrowser: Update to 0.4.0 (authored by jwb).
www/webbrowser: Update to 0.4.0
Mon, Feb 3, 3:48 PM
jwb committed R11:4f5877361b25: devel/libgamepad: Update to 0.1.2.4 (authored by jwb).
devel/libgamepad: Update to 0.1.2.4
Mon, Feb 3, 3:39 PM

Wed, Jan 29

jwb committed R11:bb5aff4439a5: biology/sra-tools: Update to 3.2.0 (authored by jwb).
biology/sra-tools: Update to 3.2.0
Wed, Jan 29, 8:20 PM

Sat, Jan 25

jwb committed R11:2889989be020: biology/mmseqs2: Update to 17.b804.f (authored by jwb).
biology/mmseqs2: Update to 17.b804.f
Sat, Jan 25, 1:24 PM

Tue, Jan 21

jwb committed R11:88365ea6e44a: science/packmol: Update to 20.15.3 (authored by jwb).
science/packmol: Update to 20.15.3
Tue, Jan 21, 3:19 PM

Jan 20 2025

jwb committed R11:e241945e9d86: devel/R-cran-optparse: Update to 1.7.5 (authored by jwb).
devel/R-cran-optparse: Update to 1.7.5
Jan 20 2025, 7:35 PM

Jan 19 2025

jwb committed R11:cad392241a59: biology/subread: Update to 2.0.8 (authored by jwb).
biology/subread: Update to 2.0.8
Jan 19 2025, 12:50 PM

Jan 17 2025

jwb committed R11:e3e3bee19927: biology/stacks: Update to 2.68 (authored by jwb).
biology/stacks: Update to 2.68
Jan 17 2025, 10:40 PM

Jan 16 2025

jwb committed R11:695d1ac4d136: biology/py-bcbio-gff: Update to 0.7.1 (authored by jwb).
biology/py-bcbio-gff: Update to 0.7.1
Jan 16 2025, 1:00 PM
jwb committed R11:25e2eac767b4: biology/bbmap: Update to 39.15 (authored by jwb).
biology/bbmap: Update to 39.15
Jan 16 2025, 12:42 PM

Jan 15 2025

jwb committed R11:4fd08b5074ce: biology/mmseqs2: Update to 16.747.c6 (authored by jwb).
biology/mmseqs2: Update to 16.747.c6
Jan 15 2025, 3:08 PM

Jan 14 2025

jwb committed R11:b324d354c77d: biology/ncbi-blast+: Update to 2.16.0 (authored by jwb).
biology/ncbi-blast+: Update to 2.16.0
Jan 14 2025, 5:47 PM
jwb committed R11:b79289d3706a: archivers/vbz-compression: Update to 1.0.12 (authored by jwb).
archivers/vbz-compression: Update to 1.0.12
Jan 14 2025, 2:22 PM
jwb committed R11:ddf239b5eee8: archivers/streamvbyte: Update to 2.0.0 (authored by jwb).
archivers/streamvbyte: Update to 2.0.0
Jan 14 2025, 1:13 PM

Jan 13 2025

jwb committed R11:1f224e0bb61a: biology/bbmap: Update to 39.14 (authored by jwb).
biology/bbmap: Update to 39.14
Jan 13 2025, 9:57 PM
jwb committed R11:3258874a89d6: science/csvtk: Update to 0.32.0 (authored by jwb).
science/csvtk: Update to 0.32.0
Jan 13 2025, 1:44 PM

Dec 29 2024

jwb committed R11:cafc58d02dee: biology/vsearch: Update to 2.29.2 (authored by jwb).
biology/vsearch: Update to 2.29.2
Dec 29 2024, 8:59 PM

Dec 12 2024

jwb committed R11:1f91b7d817f6: biology/py-multiqc: Add missing py-natsort RUN_DEPEND (authored by jwb).
biology/py-multiqc: Add missing py-natsort RUN_DEPEND
Dec 12 2024, 2:53 PM
jwb committed R11:7e69f83edba6: graphics/py-spectra: Add missing py-colormath RUN_DEPEND (authored by jwb).
graphics/py-spectra: Add missing py-colormath RUN_DEPEND
Dec 12 2024, 2:46 PM

Dec 6 2024

jwb committed R11:c543b2f67456: security/hidden-lake: F2F Anonymous network based on the QB-problem (authored by jwb).
security/hidden-lake: F2F Anonymous network based on the QB-problem
Dec 6 2024, 11:18 PM
jwb committed R11:0e30cf43051d: biology/gemma: Update to 0.98.5 (authored by jwb).
biology/gemma: Update to 0.98.5
Dec 6 2024, 2:39 PM

Dec 3 2024

jwb committed R11:12b5c3c8f16f: biology/fasttree: Update to 2.1.11 (authored by jwb).
biology/fasttree: Update to 2.1.11
Dec 3 2024, 2:55 PM

Nov 28 2024

jwb committed R11:9cb153ab3484: biology/ucsc-userapps: Update to v474 (authored by jwb).
biology/ucsc-userapps: Update to v474
Nov 28 2024, 3:59 PM
jwb committed R11:1c5c1f0c3a2e: py-htseq: New maintainer (authored by jwb).
py-htseq: New maintainer
Nov 28 2024, 12:23 PM

Nov 27 2024

jwb committed R11:b07c925f99cf: biology/py-htseq: Update to 2.0.9 (authored by jwb).
biology/py-htseq: Update to 2.0.9
Nov 27 2024, 1:46 PM

Nov 25 2024

jwb committed R11:3f6b18bb3857: biology/vcflib: Update to 1.0.12 (authored by jwb).
biology/vcflib: Update to 1.0.12
Nov 25 2024, 2:50 PM

Nov 24 2024

jwb committed R11:1c58b378342d: preseq: Not for 32-bit platforms (authored by jwb).
preseq: Not for 32-bit platforms
Nov 24 2024, 1:52 PM
jwb committed R11:482229547aae: bwa: New maintainer (authored by jwb).
bwa: New maintainer
Nov 24 2024, 1:38 PM
jwb committed R11:f488a27c4d56: biology/bwa: Update to 0.7.18 (authored by jwb).
biology/bwa: Update to 0.7.18
Nov 24 2024, 1:36 PM

Nov 22 2024

jwb committed R11:ea071869c7ee: graphics/py-plotly: Fix mangled pkg-descr (authored by jwb).
graphics/py-plotly: Fix mangled pkg-descr
Nov 22 2024, 8:58 PM
jwb committed R11:af7a74db0001: biology/preseq: Predict yield of distinct reads from a genomic library (authored by jwb).
biology/preseq: Predict yield of distinct reads from a genomic library
Nov 22 2024, 8:36 PM

Nov 21 2024

jwb committed R11:b52db326a636: biology/py-multiqc: Update to 1.25.2 (authored by jwb).
biology/py-multiqc: Update to 1.25.2
Nov 21 2024, 3:06 PM
jwb committed R11:c45dd57f7783: sysutils/devd-mount: CONFLICTS -> CONFLICTS_INSTALL (authored by jwb).
sysutils/devd-mount: CONFLICTS -> CONFLICTS_INSTALL
Nov 21 2024, 1:36 PM
jwb committed R11:628057b37dd8: filesystems/automount: Add CONFLICTS_INSTALL=devd-mount (authored by jwb).
filesystems/automount: Add CONFLICTS_INSTALL=devd-mount
Nov 21 2024, 1:34 PM
jwb committed R11:89d7d886562b: sysutils/devd-mount: Add CONFLICTS=automount (authored by jwb).
sysutils/devd-mount: Add CONFLICTS=automount
Nov 21 2024, 1:21 PM

Nov 19 2024

jwb committed R11:0569f9b878c0: deskutils/freebsd-update-notify: Update to 0.1.1.11 (authored by jwb).
deskutils/freebsd-update-notify: Update to 0.1.1.11
Nov 19 2024, 12:17 AM

Nov 17 2024

jwb committed R11:2c0b2c08a023: biology/sra-tools: Update to 3.1.1 (authored by jwb).
biology/sra-tools: Update to 3.1.1
Nov 17 2024, 11:44 PM
jwb committed R11:1d5f35837c78: deskutils/freebsd-update-notify: Update to 0.1.1.8 (authored by jwb).
deskutils/freebsd-update-notify: Update to 0.1.1.8
Nov 17 2024, 3:36 PM
jwb committed R11:1e15e2444825: deskutils/freebsd-update-notify: Update to 0.1.1.7 (authored by jwb).
deskutils/freebsd-update-notify: Update to 0.1.1.7
Nov 17 2024, 12:57 PM

Nov 16 2024

jwb committed R11:c5ab2a593af4: biology/sra-tools: Quick fix to unbreak build (authored by jwb).
biology/sra-tools: Quick fix to unbreak build
Nov 16 2024, 2:58 PM
jwb committed R11:c4c5b085262d: biology/fastp: Update to 0.24.0 (authored by jwb).
biology/fastp: Update to 0.24.0
Nov 16 2024, 1:13 PM
jwb committed R11:3f037ab2522e: biology/py-multiqc: Update to 1.25.1 (authored by jwb).
biology/py-multiqc: Update to 1.25.1
Nov 16 2024, 1:29 AM

Nov 15 2024

jwb committed R11:2ee19ca7f85a: graphics/py-plotly: Update to 5.24.1 (authored by jwb).
graphics/py-plotly: Update to 5.24.1
Nov 15 2024, 10:28 PM
jwb committed R11:3c6d6968d713: sysutils/devd-mount: Update to 0.2.0 (authored by jwb).
sysutils/devd-mount: Update to 0.2.0
Nov 15 2024, 12:39 PM
jwb committed R11:d4aaf0577e08: deskutils/qmediamanager: Update to 0.1.2 (authored by jwb).
deskutils/qmediamanager: Update to 0.1.2
Nov 15 2024, 12:33 PM

Nov 8 2024

jwb committed R11:197d365d40dc: biology/biostar-tools: Update to 2.0 (authored by jwb).
biology/biostar-tools: Update to 2.0
Nov 8 2024, 12:45 AM

Nov 7 2024

jwb committed R11:04d8b3b43354: biology/ucsc-userapps: Change license to MIT (authored by jwb).
biology/ucsc-userapps: Change license to MIT
Nov 7 2024, 11:42 PM
jwb committed R11:aaa110d4b8fe: biology/ucsc-userapps: Update to 472 (authored by jwb).
biology/ucsc-userapps: Update to 472
Nov 7 2024, 1:28 PM

Nov 3 2024

jwb committed R11:268209328697: science/csvtk: Update to 0.31.0 (authored by jwb).
science/csvtk: Update to 0.31.0
Nov 3 2024, 12:20 PM

Nov 2 2024

jwb committed R11:e68ca5734bd8: math/py-hmmlearn: Update to 0.3.3 (authored by jwb).
math/py-hmmlearn: Update to 0.3.3
Nov 2 2024, 12:31 PM

Oct 29 2024

jwb committed R11:9552b6acce7f: deskutils/coregarage: Update to 4.5.0 (authored by jwb).
deskutils/coregarage: Update to 4.5.0
Oct 29 2024, 2:34 PM
jwb committed R11:16f1d251ee48: x11/coreterminal: Update to 4.5.0 (authored by jwb).
x11/coreterminal: Update to 4.5.0
Oct 29 2024, 2:34 PM
jwb committed R11:9e28e01ff1f1: deskutils/libcprime: Update to 4.5.0 (authored by jwb).
deskutils/libcprime: Update to 4.5.0
Oct 29 2024, 2:33 PM

Oct 27 2024

jwb committed R11:6318e0f3affb: biology/vsearch: Update to 2.29.1 (authored by jwb).
biology/vsearch: Update to 2.29.1
Oct 27 2024, 10:52 PM

Oct 25 2024

jwb committed R11:3f1e2320ccc8: sysutils/auto-admin: Update to 0.8.0.50 (authored by jwb).
sysutils/auto-admin: Update to 0.8.0.50
Oct 25 2024, 12:07 PM
jwb committed R11:0f684dc168b5: sysutils/auto-admin: Update to 0.8.0.50 (authored by jwb).
sysutils/auto-admin: Update to 0.8.0.50
Oct 25 2024, 12:06 PM

Oct 24 2024

jwb committed R11:a11fc4771c87: biology/mca-calling: Core tools for mCA event calling (authored by jwb).
biology/mca-calling: Core tools for mCA event calling
Oct 24 2024, 1:33 PM

Oct 21 2024

jwb committed R11:9c84b1d1c88b: biology/vsearch: Update to 2.29.0 (authored by jwb).
biology/vsearch: Update to 2.29.0
Oct 21 2024, 8:17 PM

Oct 18 2024

jwb committed R11:0ece2dbac79c: biology/trimadap: Update to 0.1.4 (authored by jwb).
biology/trimadap: Update to 0.1.4
Oct 18 2024, 11:40 AM

Oct 16 2024

jwb added a comment to D47129: biology/trimadap: port to armv7/aarch64.

I tested on aarch64 using SIMDE. See https://github.com/outpaddling/freebsd-ports-wip/tree/master/trimadap, and let me know if it works on arm7.

Oct 16 2024, 8:32 PM
jwb added a comment to D47128: biology/fermi-lite: port to armv7/aarch64.

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.

Oct 16 2024, 8:16 PM

Oct 15 2024

jwb added a comment to D47128: biology/fermi-lite: port to armv7/aarch64.

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.

Oct 15 2024, 11:15 PM
jwb added a comment to D47129: biology/trimadap: port to armv7/aarch64.

Did you consider using devel/simde? That's usually how I get around this sort of issue.

Oct 15 2024, 9:33 PM
jwb added a comment to D47128: biology/fermi-lite: port to armv7/aarch64.

Did you consider using devel/simde? That's usually how I get around this sort of issue.

Oct 15 2024, 9:33 PM

Oct 9 2024

jwb committed R11:6a3ed7c42449: biology/bcftools: Update to 1.21 (authored by jwb).
biology/bcftools: Update to 1.21
Oct 9 2024, 10:23 PM
jwb committed R11:384625e2db65: biology/bcf-score: Update to 1.20 (authored by jwb).
biology/bcf-score: Update to 1.20
Oct 9 2024, 10:23 PM
jwb committed R11:f3b6d6f5f45c: biology/bio-mocha: Update to 1.20 (authored by jwb).
biology/bio-mocha: Update to 1.20
Oct 9 2024, 10:23 PM
jwb committed R11:c9894f60091b: biology/samtools: Update to 1.21 (authored by jwb).
biology/samtools: Update to 1.21
Oct 9 2024, 10:23 PM
jwb committed R11:aafe5d31c5f3: biology/htslib: Update to 1.21 (authored by jwb).
biology/htslib: Update to 1.21
Oct 9 2024, 10:23 PM

Sep 19 2024

jwb committed R11:c449c3e4774f: biology/kallisto: Update to 0.51.1,1 (authored by jwb).
biology/kallisto: Update to 0.51.1,1
Sep 19 2024, 10:48 PM

Sep 14 2024

jwb committed R11:fbb86e94a87c: biology/py-macs3: Update to 3.0.2 (authored by jwb).
biology/py-macs3: Update to 3.0.2
Sep 14 2024, 1:24 PM
jwb committed R11:71b1f8dd1923: math/py-hmmlearn: Update to 0.3.2 (authored by jwb).
math/py-hmmlearn: Update to 0.3.2
Sep 14 2024, 1:07 PM

Aug 7 2024

jwb committed R11:e57dda5999ac: sysutils/desktop-installer: Update to 1.0.0 (authored by jwb).
sysutils/desktop-installer: Update to 1.0.0
Aug 7 2024, 1:51 PM

Jul 27 2024

jwb committed R11:771236eb8e1a: biology/kallisto: Update to 0.51.0,1 (authored by jwb).
biology/kallisto: Update to 0.51.0,1
Jul 27 2024, 12:04 PM

Jul 25 2024

jwb committed R11:19eb57fb905e: biology/minimap2: Add NOT_FOR_ARCHS for most 32-bit processors (authored by jwb).
biology/minimap2: Add NOT_FOR_ARCHS for most 32-bit processors
Jul 25 2024, 1:09 PM

Jul 20 2024

jwb committed R11:f84c63104e8c: biology/minimap2: Add NOT_FOR_ARCHS for most 32-bit processors (authored by jwb).
biology/minimap2: Add NOT_FOR_ARCHS for most 32-bit processors
Jul 20 2024, 7:57 PM

Jul 14 2024

jwb committed R11:df8deb76eab2: x11/lumina-coreutils: More targeted WWW (authored by jwb).
x11/lumina-coreutils: More targeted WWW
Jul 14 2024, 8:38 PM
jwb committed R11:74df0bf1f83e: x11/lumina: More targeted WWW (authored by jwb).
x11/lumina: More targeted WWW
Jul 14 2024, 8:38 PM
jwb committed R11:e14463bc49db: x11/lumina-core: More targeted WWW (authored by jwb).
x11/lumina-core: More targeted WWW
Jul 14 2024, 8:38 PM
jwb committed R11:9b29e4885b0f: deskutils/lumina-photo: More targeted WWW (authored by jwb).
deskutils/lumina-photo: More targeted WWW
Jul 14 2024, 8:38 PM
jwb committed R11:3b1e379e62f1: deskutils/lumina-screenshot: More targeted WWW (authored by jwb).
deskutils/lumina-screenshot: More targeted WWW
Jul 14 2024, 8:38 PM
jwb committed R11:b28e7f3818d5: deskutils/lumina-textedit: More targeted WWW (authored by jwb).
deskutils/lumina-textedit: More targeted WWW
Jul 14 2024, 8:38 PM