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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 (368 w, 1 d)

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

Recent Activity

Thu, Dec 12

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
Thu, Dec 12, 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
Thu, Dec 12, 2:46 PM

Fri, Dec 6

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
Fri, Dec 6, 11:18 PM
jwb committed R11:0e30cf43051d: biology/gemma: Update to 0.98.5 (authored by jwb).
biology/gemma: Update to 0.98.5
Fri, Dec 6, 2:39 PM

Tue, Dec 3

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

Thu, Nov 28

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

Wed, Nov 27

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

Mon, Nov 25

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

Sun, Nov 24

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

Fri, Nov 22

jwb committed R11:ea071869c7ee: graphics/py-plotly: Fix mangled pkg-descr (authored by jwb).
graphics/py-plotly: Fix mangled pkg-descr
Fri, Nov 22, 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
Fri, Nov 22, 8:36 PM

Thu, Nov 21

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

Tue, Nov 19

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
Tue, Nov 19, 12:17 AM

Sun, Nov 17

jwb committed R11:2c0b2c08a023: biology/sra-tools: Update to 3.1.1 (authored by jwb).
biology/sra-tools: Update to 3.1.1
Sun, Nov 17, 11:44 PM

Nov 17 2024

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
jwb committed R11:d6b3c0a3b965: deskutils/lumina-mediaplayer: More targeted WWW (authored by jwb).
deskutils/lumina-mediaplayer: More targeted WWW
Jul 14 2024, 8:38 PM
jwb committed R11:dbe68a5ffc58: deskutils/lumina-pdf: More targeted WWW (authored by jwb).
deskutils/lumina-pdf: More targeted WWW
Jul 14 2024, 8:38 PM
jwb committed R11:31c068d1f320: deskutils/lumina-fileinfo: More targeted WWW (authored by jwb).
deskutils/lumina-fileinfo: More targeted WWW
Jul 14 2024, 8:38 PM
jwb committed R11:1ae45003027e: deskutils/lumina-fm: More targeted WWW (authored by jwb).
deskutils/lumina-fm: More targeted WWW
Jul 14 2024, 8:38 PM
jwb committed R11:b76f279e4759: deskutils/lumina-calculator: More targeted WWW (authored by jwb).
deskutils/lumina-calculator: More targeted WWW
Jul 14 2024, 8:38 PM
jwb committed R11:65df9e8360f7: deskutils/lumina-archiver: More targeted WWW (authored by jwb).
deskutils/lumina-archiver: More targeted WWW
Jul 14 2024, 8:38 PM

Jul 8 2024

jwb committed R11:be013acedc7d: biology/gcta: Unbreak fetch (authored by jwb).
biology/gcta: Unbreak fetch
Jul 8 2024, 11:58 PM
jwb committed R11:84a6e7ec36ea: biology/gcta: Unbreak fetch (authored by jwb).
biology/gcta: Unbreak fetch
Jul 8 2024, 10:05 PM

Jun 20 2024

jwb committed R11:1c73998d3240: deskutils/freebsd-update-notify: Update to 0.1.1.6 (authored by jwb).
deskutils/freebsd-update-notify: Update to 0.1.1.6
Jun 20 2024, 8:28 PM

Jun 3 2024

jwb committed R11:155267db532b: biology/py-pywgsim: Limit to python 3.10 (authored by jwb).
biology/py-pywgsim: Limit to python 3.10
Jun 3 2024, 11:43 AM
jwb committed R11:b8732315154d: biology/biostar-tools: Update to 1.11 (authored by jwb).
biology/biostar-tools: Update to 1.11
Jun 3 2024, 11:39 AM

May 28 2024

jwb committed R11:3bf602d2a7d0: biology/gcta: Unbreak build on 14.x aarch64 (authored by jwb).
biology/gcta: Unbreak build on 14.x aarch64
May 28 2024, 9:27 PM
jwb committed R11:b1e94269b6b8: biology/stacks: Unbreak build on aarch64 (authored by jwb).
biology/stacks: Unbreak build on aarch64
May 28 2024, 9:18 PM
jwb committed R11:859980f9d8c3: biology/minimap2: Unbreak build on aarch64 (authored by jwb).
biology/minimap2: Unbreak build on aarch64
May 28 2024, 9:07 PM

May 24 2024

jwb committed R11:4503f388135a: biology/bowtie2: Update to 2.5.4 (authored by jwb).
biology/bowtie2: Update to 2.5.4
May 24 2024, 11:34 AM

May 19 2024

jwb committed R11:f0bca8e2ac6a: biology/ad2vcf: Update to 0.1.6.19 (authored by jwb).
biology/ad2vcf: Update to 0.1.6.19
May 19 2024, 1:42 PM
jwb committed R11:93db8fd309bc: biology/biolibc: Update to 0.2.6.4 (authored by jwb).
biology/biolibc: Update to 0.2.6.4
May 19 2024, 1:40 PM
jwb committed R11:83ca8e890206: x11/lumina-core: Update to 1.6.2_10 (authored by jwb).
x11/lumina-core: Update to 1.6.2_10
May 19 2024, 1:39 PM

May 5 2024

jwb committed R11:94ae98221aa5: biology/star: Use EXTRACT_AFTER_ARGS to omit unused htslib dir (authored by jwb).
biology/star: Use EXTRACT_AFTER_ARGS to omit unused htslib dir
May 5 2024, 3:00 PM
jwb committed R11:5d736fc85e42: biology/kallisto: Use EXTRACT_AFTER_ARGS to omit unused htslib dir (authored by jwb).
biology/kallisto: Use EXTRACT_AFTER_ARGS to omit unused htslib dir
May 5 2024, 2:47 PM

May 1 2024

jwb committed R11:410ef5f336a5: sysutils/auto-admin: Update to 0.8.0.33 (authored by jwb).
sysutils/auto-admin: Update to 0.8.0.33
May 1 2024, 1:55 PM
jwb committed R11:28e6daedef5c: sysutils/auto-admin: Update to 0.8.0.33 (authored by jwb).
sysutils/auto-admin: Update to 0.8.0.33
May 1 2024, 1:54 PM
jwb committed R11:d43c48f14014: biology/vsearch: Update to 2.28.1 (authored by jwb).
biology/vsearch: Update to 2.28.1
May 1 2024, 1:41 PM

Apr 22 2024

jwb committed R11:1de14dfc3b4c: biology/wfa2-lib: Update to 2.3.5 (authored by jwb).
biology/wfa2-lib: Update to 2.3.5
Apr 22 2024, 12:42 PM
jwb committed R11:86c8816c2c85: biology/vcflib: Update to 1.0.10 (authored by jwb).
biology/vcflib: Update to 1.0.10
Apr 22 2024, 12:42 PM

Apr 18 2024

jwb committed R11:6308879ec20d: biology/py-macs3: Mark not for i386 (authored by jwb).
biology/py-macs3: Mark not for i386
Apr 18 2024, 11:04 PM

Apr 17 2024

jwb committed R11:507fa8ab3709: biology/minimap2: Fix man prefix (authored by jwb).
biology/minimap2: Fix man prefix
Apr 17 2024, 10:53 PM

Apr 10 2024

jwb committed R11:fa60f361e810: biology/py-dnaio: Release to ports@ (authored by jwb).
biology/py-dnaio: Release to ports@
Apr 10 2024, 11:43 PM
jwb committed R11:8efa6a228307: biology/minimap2: Update to 2.28 (authored by jwb).
biology/minimap2: Update to 2.28
Apr 10 2024, 12:29 PM

Apr 8 2024

jwb committed R11:3d100fcffcdb: biology/vsearch: Update to 2.27.1 (authored by jwb).
biology/vsearch: Update to 2.27.1
Apr 8 2024, 9:45 PM

Apr 6 2024

jwb committed R11:7045d13e4cdf: biology/py-cutadapt: Release to ports@ (authored by jwb).
biology/py-cutadapt: Release to ports@
Apr 6 2024, 12:12 AM
jwb committed R11:f86a4bf87948: biology/p5-TrimGalore: Release to ports@ (authored by jwb).
biology/p5-TrimGalore: Release to ports@
Apr 6 2024, 12:12 AM
jwb committed R11:2bce91331ff3: biology/trimmomatic: Release to ports@ (authored by jwb).
biology/trimmomatic: Release to ports@
Apr 6 2024, 12:12 AM
jwb committed R11:204123b152c7: archivers/py-xopen: Release to ports@ (authored by jwb).
archivers/py-xopen: Release to ports@
Apr 6 2024, 12:12 AM

Apr 2 2024

jwb committed R11:7b4311b4ff25: sysutils/auto-admin: Update to 0.8.0.27 (authored by jwb).
sysutils/auto-admin: Update to 0.8.0.27
Apr 2 2024, 1:28 PM