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jwb (jwb@freebsd.org)
HPC Systems Programmer

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User Since
Nov 27 2017, 4:37 PM (69 w, 22 h)

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

Recent Activity

Sun, Mar 24

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

Answered my own question + received some feedback.

Sun, Mar 24, 8:46 PM
jwb committed rP496774: archivers/py-xopen: Upgrade to 0.5.0.
archivers/py-xopen: Upgrade to 0.5.0
Sun, Mar 24, 8:05 PM
jwb committed rP496770: biology/py-dnaio: Read and write FASTQ and FASTA.
biology/py-dnaio: Read and write FASTQ and FASTA
Sun, Mar 24, 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.

Sun, Mar 24, 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.

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

Mon, Mar 18

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

Fri, Mar 15

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

Tue, Feb 26

jwb committed rP493930: sysutils/desktop-installer: PPC64 fixes, user guidance for drm-kmod.
sysutils/desktop-installer: PPC64 fixes, user guidance for drm-kmod
Tue, Feb 26, 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
Tue, Feb 26, 2:04 AM

Sun, Feb 24

jwb committed rP493810: kallisto: Upgrade to 0.45.1, unbundle hstlib.
kallisto: Upgrade to 0.45.1, unbundle hstlib
Sun, Feb 24, 8:32 PM
jwb committed rP493769: biology/unanimity: Upgrade to 3.4.1.
biology/unanimity: Upgrade to 3.4.1
Sun, Feb 24, 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
jwb created D16902: biology/unanimity: Upgrade to latest release, soften dep version requirements.
Aug 25 2018, 9:15 PM

Aug 4 2018

jwb committed rP476330: biology/vcftools: Update to 0.1.16, a security release.
biology/vcftools: Update to 0.1.16, a security release
Aug 4 2018, 1:29 AM
jwb closed D16587: biology/vcftools: Update to 0.1.16, a security release.
Aug 4 2018, 1:29 AM

Aug 3 2018

jwb created D16587: biology/vcftools: Update to 0.1.16, a security release.
Aug 3 2018, 9:14 PM

Jul 7 2018

jwb committed rP474083: archivers/py-xopen: Upgrade to 0.3.5.
archivers/py-xopen: Upgrade to 0.3.5
Jul 7 2018, 1:41 PM
jwb closed D16170: archivers/py-xopen: Upgrade to 0.3.5.
Jul 7 2018, 1:41 PM
jwb created D16170: archivers/py-xopen: Upgrade to 0.3.5.
Jul 7 2018, 2:47 AM

Jun 27 2018

jwb added a comment to D15981: comms/cutecom: Upgrade to 0.45.0.

Thanks for clarifying, I've updated my checklist...

Jun 27 2018, 12:51 PM
jwb added a comment to D16024: science/paraview: Fix protobuf conflict, upgrade to 5.5.1, modernize options.

Thanks!

Jun 27 2018, 12:48 PM
jwb closed D16028: comms/cutecom: Fix WRKSRC name.
Jun 27 2018, 2:18 AM
jwb committed rP473416: comms/cutecom: Fix WRKSRC name.
comms/cutecom: Fix WRKSRC name
Jun 27 2018, 2:18 AM
jwb created D16028: comms/cutecom: Fix WRKSRC name.
Jun 27 2018, 12:19 AM
jwb committed rP473414: science/paraview: Fix protobuf conflict, upgrade to 5.5.1, modernize options.
science/paraview: Fix protobuf conflict, upgrade to 5.5.1, modernize options
Jun 27 2018, 12:04 AM
jwb closed D16024: science/paraview: Fix protobuf conflict, upgrade to 5.5.1, modernize options.
Jun 27 2018, 12:04 AM

Jun 26 2018

jwb added a comment to D16024: science/paraview: Fix protobuf conflict, upgrade to 5.5.1, modernize options.

Yeah, I got that, but now I'm uncertain about exactly which OPTIONS features require it. The handbook isn't clear and the mk file is too big to study in detail. I'll just try without it and add when needed, I guess.

Jun 26 2018, 11:57 PM
jwb updated the diff for D16024: science/paraview: Fix protobuf conflict, upgrade to 5.5.1, modernize options.

Apparently so. Never would have thought of it. The handbook is vague about
this, but it seems to work fine. I ran a make clean rmconfig configure
with 3 different options combos and got expected results.

Jun 26 2018, 11:34 PM
jwb created D16024: science/paraview: Fix protobuf conflict, upgrade to 5.5.1, modernize options.
Jun 26 2018, 7:05 PM
jwb closed D15981: comms/cutecom: Upgrade to 0.45.0.

I put the wrong revision URL in the commit, so it did not close automatically.

Jun 26 2018, 6:57 PM

Jun 24 2018

jwb committed rP473198: comms/cutecom: Upgrade to 0.45.0.
comms/cutecom: Upgrade to 0.45.0
Jun 24 2018, 1:18 PM
jwb added a comment to D15981: comms/cutecom: Upgrade to 0.45.0.

Thanks for digging up the old link. I already did change PORTNAME back to cutecom, as @mat's comment would seem to suggest. Also I recall the conversation going to email and getting a little heated, but @mat's take seemed reasonable to me so I've been trying to follow it.

Jun 24 2018, 1:18 AM

Jun 23 2018

jwb updated the diff for D15981: comms/cutecom: Upgrade to 0.45.0.

I recall the conversation, but I think it ended with a lack of consensus
even among senior developers. The handbook still doesn't clarify this.
I'm agnostic...

Jun 23 2018, 8:39 PM
jwb created D15981: comms/cutecom: Upgrade to 0.45.0.
Jun 23 2018, 12:59 PM

Jun 16 2018

jwb committed rP472560: biology/bedtools: Fix Makefile to respect PREFIX.
biology/bedtools: Fix Makefile to respect PREFIX
Jun 16 2018, 5:55 PM
jwb closed D15851: biology/bedtools: Fix Makefile to respect PREFIX.
Jun 16 2018, 5:55 PM
jwb added a comment to D15851: biology/bedtools: Fix Makefile to respect PREFIX.

I think that's a good idea and certainly won't hurt. I'll add it to the commit. Thanks...

Jun 16 2018, 5:52 PM
jwb created D15851: biology/bedtools: Fix Makefile to respect PREFIX.
Jun 16 2018, 2:58 PM

May 30 2018

jwb committed rP471151: sysutils/desktop-installer: Add KDE5 support, more default video drivers.
sysutils/desktop-installer: Add KDE5 support, more default video drivers
May 30 2018, 7:14 PM
jwb closed D15622: sysutils/desktop-installer: Add KDE5 support, more default video drivers.
May 30 2018, 7:14 PM
jwb updated the diff for D15622: sysutils/desktop-installer: Add KDE5 support, more default video drivers.

Another distracted error. The good news is, I'll have fewer distractions once this is committed. ;-)

May 30 2018, 7:10 PM
jwb created D15622: sysutils/desktop-installer: Add KDE5 support, more default video drivers.
May 30 2018, 6:59 PM
jwb added a comment to D15619: auto-admin: Add support for AD authentication, factor out pkgsrc scripts.

Yeah, I knew about the done box. Sorry, just distracted today.

May 30 2018, 6:49 PM
jwb committed rP471149: auto-admin: Add support for AD authentication, factor out pkgsrc scripts.
auto-admin: Add support for AD authentication, factor out pkgsrc scripts
May 30 2018, 6:48 PM
jwb closed D15619: auto-admin: Add support for AD authentication, factor out pkgsrc scripts.
May 30 2018, 6:48 PM
jwb updated the diff for D15619: auto-admin: Add support for AD authentication, factor out pkgsrc scripts.

Better yet, I'm just going to stop generating manpages for undocumented
scripts. I need to catch up on the documentation as well as separate it out.
I'd like to autogenerate man pages for each script, but haven't found a good
tool yet. Doxygen is nice for HTML but stinks at man pages.

May 30 2018, 6:32 PM
jwb added a comment to D15619: auto-admin: Add support for AD authentication, factor out pkgsrc scripts.

Yes, it's correct. Currently there is one man page covering all scripts (at least the ones that are documented).

May 30 2018, 5:17 PM
jwb updated the diff for D15619: auto-admin: Add support for AD authentication, factor out pkgsrc scripts.

Silence mkdir

May 30 2018, 5:12 PM
jwb created D15619: auto-admin: Add support for AD authentication, factor out pkgsrc scripts.
May 30 2018, 4:47 PM

May 21 2018

jwb committed rP470582: biology/clustal-omega: Multiple alignment of nucleic acid and protein, replaces….
biology/clustal-omega: Multiple alignment of nucleic acid and protein, replaces…
May 21 2018, 10:15 PM