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jwb (jwb@freebsd.org)
HPC Systems Programmer

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User Details

User Since
Nov 27 2017, 4:37 PM (85 w, 2 d)

Systems manager and facilitator for Research Computing at the University of Wisconsin -- Milwaukee

Recent Activity

Fri, Jul 12

jwb committed rP506497: ncbi-blast+: Unbreak build with gcc8 following gcc9 patch.
ncbi-blast+: Unbreak build with gcc8 following gcc9 patch
Fri, Jul 12, 11:58 PM

Thu, Jul 11

jwb committed rP506409: ncbi-blast+: Fix build with gcc9.
ncbi-blast+: Fix build with gcc9
Thu, Jul 11, 1:53 PM

Tue, Jun 18

jwb committed rP504496: science/afni: Upgrade to 19.1.20.
science/afni: Upgrade to 19.1.20
Tue, Jun 18, 7:01 PM

Jun 14 2019

jwb committed rP504153: biology/ncbi-blast+: Fix build on powerpc64, add run dep for update_blastdb.pl.
biology/ncbi-blast+: Fix build on powerpc64, add run dep for update_blastdb.pl
Jun 14 2019, 12:38 AM
jwb committed rP504151: sysutils/slurm-wlm: Revert previous change enabling Linux option by default.
sysutils/slurm-wlm: Revert previous change enabling Linux option by default
Jun 14 2019, 12:21 AM

Jun 13 2019

jwb committed rP504147: sysutils/slurm-wlm: Enable jobacct_gather/linux by default.
sysutils/slurm-wlm: Enable jobacct_gather/linux by default
Jun 13 2019, 11:53 PM

Jun 12 2019

jwb committed rP504047: biology/ncbi-blast+: Upgrade to 2.9.0.
biology/ncbi-blast+: Upgrade to 2.9.0
Jun 12 2019, 11:53 PM
jwb committed rP504011: biology/kallisto: Upgrade to 0.46.0.
biology/kallisto: Upgrade to 0.46.0
Jun 12 2019, 3:25 PM

Jun 8 2019

jwb committed rP503747: science/afni: Upgrade to 19.1.18.
science/afni: Upgrade to 19.1.18
Jun 8 2019, 7:14 PM

Jun 1 2019

jwb committed rP503233: science/afni: Upgrade to 19.1.14.
science/afni: Upgrade to 19.1.14
Jun 1 2019, 1:00 PM

May 26 2019

jwb committed rP502673: biology/bolt-lmm: Mixed model association testing and variance component….
biology/bolt-lmm: Mixed model association testing and variance component…
May 26 2019, 3:37 AM

May 22 2019

jwb committed rP502266: science/afni: Upgrade to 19.1.10.
science/afni: Upgrade to 19.1.10
May 22 2019, 12:44 PM

May 20 2019

jwb committed rP502179: sysutils/slurm-wlm: Remove redundant USE_GCC.
sysutils/slurm-wlm: Remove redundant USE_GCC
May 20 2019, 11:47 PM
jwb committed rP502178: biology/fastp: Remove redundant USE_GCC.
biology/fastp: Remove redundant USE_GCC
May 20 2019, 11:41 PM
jwb committed rP502158: science/afni: Upgrade to 19.1.08.
science/afni: Upgrade to 19.1.08
May 20 2019, 7:36 PM

May 18 2019

jwb committed rP501990: biology/gemma: Lowercase PORTNAME, remove unnecesary USE_GCC.
biology/gemma: Lowercase PORTNAME, remove unnecesary USE_GCC
May 18 2019, 10:41 PM

May 17 2019

jwb committed rP501873: biology/gemma: Genome-wide Efficient Mixed Model Association.
biology/gemma: Genome-wide Efficient Mixed Model Association
May 17 2019, 2:45 PM

May 15 2019

jwb committed rP501674: sysutils/slurm-wlm: Upgrade to 18.08.7.
sysutils/slurm-wlm: Upgrade to 18.08.7
May 15 2019, 1:34 AM

May 13 2019

jwb committed rP501578: biology/jellyfish: Upgrade to 2.2.10, patch for powerpc64.
biology/jellyfish: Upgrade to 2.2.10, patch for powerpc64
May 13 2019, 4:23 PM

May 11 2019

jwb committed rP501259: biology/vsearch: Update to 2.13.4.
biology/vsearch: Update to 2.13.4
May 11 2019, 1:42 PM
jwb committed rP501207: biology/trimadap: Mark only for amd64 and i386.
biology/trimadap: Mark only for amd64 and i386
May 11 2019, 12:18 AM

May 10 2019

jwb committed rP501200: biology/stacks: Remove obsolete pkg-message regarding web interface.
biology/stacks: Remove obsolete pkg-message regarding web interface
May 10 2019, 9:16 PM
jwb committed rP501199: biology/stacks: Upgrade to 2.4.
biology/stacks: Upgrade to 2.4
May 10 2019, 9:04 PM

May 9 2019

jwb committed rP501148: biology/vsearch: Remove powerpc64 support.
biology/vsearch: Remove powerpc64 support
May 9 2019, 10:12 PM
jwb committed rP501147: biology/vsearch: Versatile open-source tool for metagenomics.
biology/vsearch: Versatile open-source tool for metagenomics
May 9 2019, 9:29 PM

May 5 2019

jwb committed rP500860: biology/minimap2: Upgrade to 2.17.
biology/minimap2: Upgrade to 2.17
May 5 2019, 2:56 PM

May 4 2019

jwb committed rP500812: biology/ddocent: Upgrade to 2.7.8.
biology/ddocent: Upgrade to 2.7.8
May 4 2019, 3:09 PM
jwb committed rP500770: biology/fastp: Respect WITH_DEBUG - do not strip binary.
biology/fastp: Respect WITH_DEBUG - do not strip binary
May 4 2019, 2:07 AM

May 3 2019

jwb committed rP500737: biology/fastp: Ultra-fast all-in-one FASTQ preprocessor.
biology/fastp: Ultra-fast all-in-one FASTQ preprocessor
May 3 2019, 2:42 PM

May 2 2019

jwb committed rP500629: biology/star: Force newer GCC on platforms with GCC 4.2 base.
biology/star: Force newer GCC on platforms with GCC 4.2 base
May 2 2019, 12:40 AM

Apr 27 2019

jwb committed rP500187: biology/py-cutadapt: Upgrade to 2.3.
biology/py-cutadapt: Upgrade to 2.3
Apr 27 2019, 1:26 AM
jwb committed rP500186: archivers/py-xopen: Upgrade to 0.5.1.
archivers/py-xopen: Upgrade to 0.5.1
Apr 27 2019, 1:22 AM

Apr 24 2019

jwb committed rP499895: biology/minimap2: Pairwise aligner for genomic and spliced nucleotide sequences.
biology/minimap2: Pairwise aligner for genomic and spliced nucleotide sequences
Apr 24 2019, 6:04 PM
jwb committed rP499873: biology/bowtie2: Clarify CPU-specificity.
biology/bowtie2: Clarify CPU-specificity
Apr 24 2019, 5:41 PM

Apr 23 2019

jwb committed rP499763: biology/star: Modify PKGBASE to avoid conflict with archivers/star.
biology/star: Modify PKGBASE to avoid conflict with archivers/star
Apr 23 2019, 3:03 PM

Apr 21 2019

jwb committed rP499592: biology/star: Spliced Transcripts Alignment to a Reference.
biology/star: Spliced Transcripts Alignment to a Reference
Apr 21 2019, 8:31 PM
jwb committed rP499544: biology/bowtie2: Upgrade to 2.3.5.1.
biology/bowtie2: Upgrade to 2.3.5.1
Apr 21 2019, 3:23 PM

Apr 18 2019

jwb committed rP499251: biology/canu: Fix build on powerpc64 and aarch64.
biology/canu: Fix build on powerpc64 and aarch64
Apr 18 2019, 12:16 PM

Mar 24 2019

jwb committed rP496785: biology/p5-TrimGalore: Upgrade to 0.6.1.
biology/p5-TrimGalore: Upgrade to 0.6.1
Mar 24 2019, 9:44 PM
jwb committed rP496783: biology/py-cutadapt: Upgrade to 2.1.
biology/py-cutadapt: Upgrade to 2.1
Mar 24 2019, 9:20 PM
jwb abandoned D19693: biology/py-dnaio: Read and write FASTQ and FASTA.

Answered my own question + received some feedback.

Mar 24 2019, 8:46 PM
jwb committed rP496774: archivers/py-xopen: Upgrade to 0.5.0.
archivers/py-xopen: Upgrade to 0.5.0
Mar 24 2019, 8:05 PM
jwb committed rP496770: biology/py-dnaio: Read and write FASTQ and FASTA.
biology/py-dnaio: Read and write FASTQ and FASTA
Mar 24 2019, 7:40 PM
jwb updated the diff for D19693: biology/py-dnaio: Read and write FASTQ and FASTA.

Thanks, checksubdirs is not mentioned in the FAQ. It just says to make
sure you don't want a repocopy instead, and use Tools/scripts/addport.

Mar 24 2019, 3:09 PM
jwb added a comment to D19693: biology/py-dnaio: Read and write FASTQ and FASTA.

Never mind the new port question, I found it in FAQ.

Mar 24 2019, 2:14 PM
jwb created D19693: biology/py-dnaio: Read and write FASTQ and FASTA.
Mar 24 2019, 12:56 PM

Mar 18 2019

jwb committed rP496155: biology/bowtie2: Upgrade to 2.3.5.
biology/bowtie2: Upgrade to 2.3.5
Mar 18 2019, 5:30 PM

Mar 15 2019

jwb committed rP495746: biology/cd-hit: Upgrade to 4.8.1.
biology/cd-hit: Upgrade to 4.8.1
Mar 15 2019, 12:00 AM

Feb 26 2019

jwb committed rP493930: sysutils/desktop-installer: PPC64 fixes, user guidance for drm-kmod.
sysutils/desktop-installer: PPC64 fixes, user guidance for drm-kmod
Feb 26 2019, 2:13 AM
jwb committed rP493929: sysutils/auto-admin: Factor code out of desktop-installer and cluster-admin.
sysutils/auto-admin: Factor code out of desktop-installer and cluster-admin
Feb 26 2019, 2:04 AM

Feb 24 2019

jwb committed rP493810: kallisto: Upgrade to 0.45.1, unbundle hstlib.
kallisto: Upgrade to 0.45.1, unbundle hstlib
Feb 24 2019, 8:32 PM
jwb committed rP493769: biology/unanimity: Upgrade to 3.4.1.
biology/unanimity: Upgrade to 3.4.1
Feb 24 2019, 4:05 PM

Feb 20 2019

jwb committed rP493403: biology/pbseqan: Mark deprecated.
biology/pbseqan: Mark deprecated
Feb 20 2019, 1:53 AM
jwb committed rP493402: biology/unanimity: Upgrade to 3.4.0.
biology/unanimity: Upgrade to 3.4.0
Feb 20 2019, 1:37 AM

Feb 19 2019

jwb committed rP493399: biology/pbbam: Upgrade to 0.18.0 release.
biology/pbbam: Upgrade to 0.18.0 release
Feb 19 2019, 11:04 PM
jwb committed rP493397: biology/pbcopper: Upgrade to 0.4.1 release.
biology/pbcopper: Upgrade to 0.4.1 release
Feb 19 2019, 10:20 PM

Feb 17 2019

jwb committed rP493182: biology/pbseqan: Minor upgrade to latest commit.
biology/pbseqan: Minor upgrade to latest commit
Feb 17 2019, 7:31 PM

Jan 21 2019

jwb committed rP490857: comms/cutecom: Update pkg-descr to reflect new home.
comms/cutecom: Update pkg-descr to reflect new home
Jan 21 2019, 1:18 PM

Jan 20 2019

jwb committed rP490790: comms/cutecom: Add c++11-lang for GCC-based platforms, upgrade to 0.51.0.
comms/cutecom: Add c++11-lang for GCC-based platforms, upgrade to 0.51.0
Jan 20 2019, 2:01 PM

Jan 12 2019

jwb committed rP490062: biology/stacks: Upgrade to 2.3.
biology/stacks: Upgrade to 2.3
Jan 12 2019, 3:53 PM

Jan 11 2019

jwb committed rP489981: New port: biology/hisat2: Program for mapping next-generation sequencing reads.
New port: biology/hisat2: Program for mapping next-generation sequencing reads
Jan 11 2019, 4:02 PM

Jan 1 2019

jwb committed rP488931: biology/ncbi-blast+: Upgrade to 2.8.1.
biology/ncbi-blast+: Upgrade to 2.8.1
Jan 1 2019, 7:56 PM

Dec 28 2018

jwb committed rP488604: sysutils/desktop-installer: Add nVidia GPU detection.
sysutils/desktop-installer: Add nVidia GPU detection
Dec 28 2018, 2:57 PM
jwb committed rP488601: sysutils/auto-admin: New scripts to support of desktop-installer, cluster-admin.
sysutils/auto-admin: New scripts to support of desktop-installer, cluster-admin
Dec 28 2018, 2:06 PM

Dec 10 2018

jwb committed rP487202: sysutils/condor: Permanent fix for FreeBSD 13 and all future versions.
sysutils/condor: Permanent fix for FreeBSD 13 and all future versions
Dec 10 2018, 9:41 PM

Nov 17 2018

jwb committed rP485195: sysutils/desktop-installer: Necessary maintenance updates.
sysutils/desktop-installer: Necessary maintenance updates
Nov 17 2018, 8:40 PM
jwb committed rP485194: auto-admin: Add several scripts to support wip/cluster-admin.
auto-admin: Add several scripts to support wip/cluster-admin
Nov 17 2018, 8:33 PM

Nov 4 2018

jwb committed rP484101: science/voro++: Add shared library.
science/voro++: Add shared library
Nov 4 2018, 3:53 PM
jwb committed rP484077: biology/canu: Upgrade to 1.8, add experimental SLURM integration.
biology/canu: Upgrade to 1.8, add experimental SLURM integration
Nov 4 2018, 2:29 PM

Nov 3 2018

jwb committed rP483954: biology/bowtie: Patch for gcc8 and clean up.
biology/bowtie: Patch for gcc8 and clean up
Nov 3 2018, 11:24 PM
jwb committed rP483953: biology/bowtie: Revert previous commit with missing log message.
biology/bowtie: Revert previous commit with missing log message
Nov 3 2018, 11:16 PM
jwb committed rP483910: biology/bowtie: Patch.
biology/bowtie: Patch
Nov 3 2018, 9:10 PM

Oct 23 2018

jwb committed rP482836: biology/p5-transdecoder: Upgrade to 5.4.0.
biology/p5-transdecoder: Upgrade to 5.4.0
Oct 23 2018, 12:51 PM

Oct 22 2018

jwb committed rP482729: sysutils/desktop-installer: Fix battery monitor, install audio/lame.
sysutils/desktop-installer: Fix battery monitor, install audio/lame
Oct 22 2018, 2:29 AM
jwb closed D17643: sysutils/desktop-installer: Fix battery monitor, install audio/lame.
Oct 22 2018, 2:29 AM
jwb created D17643: sysutils/desktop-installer: Fix battery monitor, install audio/lame.
Oct 22 2018, 1:29 AM
jwb committed rP482728: sysutils/auto-admin: Improved support for desktop-installer, cluster-admin.
sysutils/auto-admin: Improved support for desktop-installer, cluster-admin
Oct 22 2018, 1:12 AM
jwb closed D17638: sysutils/auto-admin: Improved support for desktop-installer, cluster-admin.
Oct 22 2018, 1:12 AM

Oct 21 2018

jwb created D17638: sysutils/auto-admin: Improved support for desktop-installer, cluster-admin.
Oct 21 2018, 4:06 PM

Sep 30 2018

jwb committed rP480985: science/fsom: Fix build on GCC-based architectures.
science/fsom: Fix build on GCC-based architectures
Sep 30 2018, 9:41 PM
jwb closed D17366: science/fsom: Fix build on GCC-based architectures.
Sep 30 2018, 9:41 PM
jwb created D17366: science/fsom: Fix build on GCC-based architectures.
Sep 30 2018, 4:37 PM

Sep 21 2018

jwb committed rP480273: sysutils/ganglia-webfrontend: Fix known display bug in cluster view.
sysutils/ganglia-webfrontend: Fix known display bug in cluster view
Sep 21 2018, 2:57 PM
jwb closed D17264: sysutils/ganglia-webfrontend: Fix known display bug in cluster view.
Sep 21 2018, 2:57 PM

Sep 20 2018

jwb created D17264: sysutils/ganglia-webfrontend: Fix known display bug in cluster view.
Sep 20 2018, 11:03 PM
jwb committed rP480173: biology/py-cutadapt: Upgrade to 1.18.
biology/py-cutadapt: Upgrade to 1.18
Sep 20 2018, 2:11 PM
jwb closed D17099: biology/py-cutadapt: Upgrade to 1.18.
Sep 20 2018, 2:10 PM

Sep 18 2018

jwb updated the diff for D17099: biology/py-cutadapt: Upgrade to 1.18.

Cripes, I have no memory of removing that. I hope it's good now.
Let's get this one tied up and then you won't hear from me again until
I restore some order to my life... ;-)

Sep 18 2018, 11:24 PM

Sep 17 2018

jwb updated the diff for D17099: biology/py-cutadapt: Upgrade to 1.18.

Hopefully final patch for this upgrade. Added one overlooked runtime dep.

Sep 17 2018, 4:19 PM
jwb added a comment to D17099: biology/py-cutadapt: Upgrade to 1.18.

Yeah, that might be a good idea. I took this as more of a future reference tip than something urgent for this port, and I've added a note to my checklist.

Sep 17 2018, 2:09 PM
jwb added a comment to D17099: biology/py-cutadapt: Upgrade to 1.18.

The do-test target is proving a little squirrely. I'll have to come back to this when I'm not so slammed...

Sep 17 2018, 1:34 PM

Sep 10 2018

jwb updated the diff for D17099: biology/py-cutadapt: Upgrade to 1.18.

Ooops, made changes to wip instead of biology the first time.

Sep 10 2018, 1:52 PM
jwb updated the diff for D17099: biology/py-cutadapt: Upgrade to 1.18.

Good stuff, thanks guys! I added these tips to my checklist.

Sep 10 2018, 1:42 PM

Sep 9 2018

jwb created D17099: biology/py-cutadapt: Upgrade to 1.18.
Sep 9 2018, 7:15 PM

Sep 1 2018

jwb committed rP478697: biology/stacks: Enable OpenMP (oversight in previous commit).
biology/stacks: Enable OpenMP (oversight in previous commit)
Sep 1 2018, 2:14 PM
jwb closed D16973: biology/stacks: Enable OpenMP (oversight in previous commit).
Sep 1 2018, 2:14 PM
jwb updated the diff for D16973: biology/stacks: Enable OpenMP (oversight in previous commit).

Ugh, slow down Jason...

Sep 1 2018, 1:36 PM

Aug 31 2018

jwb created D16973: biology/stacks: Enable OpenMP (oversight in previous commit).
Aug 31 2018, 2:11 PM

Aug 25 2018

jwb committed rP478089: biology/unanimity: Upgrade to latest release, soften dep version requirements.
biology/unanimity: Upgrade to latest release, soften dep version requirements
Aug 25 2018, 10:55 PM
jwb closed D16902: biology/unanimity: Upgrade to latest release, soften dep version requirements.
Aug 25 2018, 10:55 PM