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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 (177 w, 3 d)

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

Recent Activity

Wed, Apr 21

jwb committed R11:3c21e709e899: biology/py-crossmap: Update to 0.5.4 (authored by jwb).
biology/py-crossmap: Update to 0.5.4
Wed, Apr 21, 1:32 PM

Mon, Apr 19

jwb committed R11:3bc87a0f1a1b: biology/snpeff: Improvements to Makefile and patches (authored by jwb).
biology/snpeff: Improvements to Makefile and patches
Mon, Apr 19, 4:42 PM

Sun, Apr 18

jwb committed R11:5164d38ee538: biology/snpeff: Genetic variant annotation and effect prediction toolbox (authored by jwb).
biology/snpeff: Genetic variant annotation and effect prediction toolbox
Sun, Apr 18, 6:47 PM
jwb committed R11:15458dfbacb8: biology/bbmap: BBMap short read aligner, and other bioinformatic tools (authored by jwb).
biology/bbmap: BBMap short read aligner, and other bioinformatic tools
Sun, Apr 18, 4:23 PM
jwb committed R11:48ddc73c5822: biology/bowtie2: Add support for powerpc64le (authored by jwb).
biology/bowtie2: Add support for powerpc64le
Sun, Apr 18, 3:54 PM
jwb committed R11:1b6e8568ce41: biology/readseq: Remove $FreeBSD$ tag inserted to silence portlint (authored by jwb).
biology/readseq: Remove $FreeBSD$ tag inserted to silence portlint
Sun, Apr 18, 2:22 PM
jwb committed R11:49a1ada63293: biology/readseq: Read and reformat biosequences, Java command-line version (authored by jwb).
biology/readseq: Read and reformat biosequences, Java command-line version
Sun, Apr 18, 1:54 PM

Fri, Apr 16

jwb committed R11:ed41b3295ccf: sysutils/linux-miniconda-installer: Aid for installing and using miniconda (authored by jwb).
sysutils/linux-miniconda-installer: Aid for installing and using miniconda
Fri, Apr 16, 4:26 PM
jwb committed R11:def843401834: sysutils/desktop-installer: Fix accidentally silenced user prompt (authored by jwb).
sysutils/desktop-installer: Fix accidentally silenced user prompt
Fri, Apr 16, 3:12 PM
jwb committed R11:0e084ddc8634: sysutils/desktop-installer: Fix accidentally silenced user prompt (authored by jwb).
sysutils/desktop-installer: Fix accidentally silenced user prompt
Fri, Apr 16, 3:07 PM

Tue, Apr 13

jwb committed R11:fd20bf82b699: biology/mothur: Update to 1.45.2 (authored by jwb).
biology/mothur: Update to 1.45.2
Tue, Apr 13, 12:30 AM

Mon, Apr 12

jwb committed R11:912872756265: biology/py-crossmap: Lift over genomics coordinates between assemblies (authored by jwb).
biology/py-crossmap: Lift over genomics coordinates between assemblies
Mon, Apr 12, 11:38 PM
jwb committed R11:dfcece22a2cb: biology/py-bigwig: Python access to bigWig files using libBigWig (authored by jwb).
biology/py-bigwig: Python access to bigWig files using libBigWig
Mon, Apr 12, 11:24 PM

Tue, Mar 30

jwb committed rP569561: biology/subread: Update to 2.0.2.
biology/subread: Update to 2.0.2
Tue, Mar 30, 3:31 PM

Fri, Mar 26

jwb committed rP569257: sysutils/auto-admin: Update to 0.7.1.2.
sysutils/auto-admin: Update to 0.7.1.2
Fri, Mar 26, 4:31 PM

Wed, Mar 24

jwb committed rP569151: biology/vsearch: Update to 2.16.0.
biology/vsearch: Update to 2.16.0
Wed, Mar 24, 6:43 PM

Mar 23 2021

jwb committed rP569036: biology/vcf2hap: Generate .hap file from VCF for haplohseq.
biology/vcf2hap: Generate .hap file from VCF for haplohseq
Mar 23 2021, 4:32 PM
jwb committed rP569033: biology/ad2vcf: Add allelic depth info from a SAM stream to a VCF file.
biology/ad2vcf: Add allelic depth info from a SAM stream to a VCF file
Mar 23 2021, 3:15 PM

Mar 21 2021

jwb committed rP568922: biology/vcf-split: Split a multi-sample VCF into single-sample VCFs.
biology/vcf-split: Split a multi-sample VCF into single-sample VCFs
Mar 21 2021, 3:18 PM
jwb committed rP568921: biology/biolibc: Low-level high-performance bioinformatics library.
biology/biolibc: Low-level high-performance bioinformatics library
Mar 21 2021, 3:10 PM

Mar 20 2021

jwb committed rP568874: biology/htslib: Update to 1.12.
biology/htslib: Update to 1.12
Mar 20 2021, 5:15 PM
jwb committed rP568867: biology/generand: Update to 0.1.2.
biology/generand: Update to 0.1.2
Mar 20 2021, 2:32 PM
jwb committed rP568866: biology/py-multiqc: Update to 1.10.
biology/py-multiqc: Update to 1.10
Mar 20 2021, 2:26 PM

Mar 15 2021

jwb committed rP568501: biology/generand: Generate random genomic data in FAST[AQ], SAM, or VCF format.
biology/generand: Generate random genomic data in FAST[AQ], SAM, or VCF format
Mar 15 2021, 8:09 PM
jwb committed rP568497: sysutils/spcm: Update to 0.5.4.
sysutils/spcm: Update to 0.5.4
Mar 15 2021, 7:38 PM
jwb committed rP568471: sysutils/desktop-installer: Update to 0.7.1.
sysutils/desktop-installer: Update to 0.7.1
Mar 15 2021, 4:43 PM
jwb committed rP568470: sysutils/auto-admin: Update to 0.7.1.
sysutils/auto-admin: Update to 0.7.1
Mar 15 2021, 4:39 PM

Mar 6 2021

jwb committed rP567503: py-cutadapt: Update to 3.3.
py-cutadapt: Update to 3.3
Mar 6 2021, 5:55 PM

Mar 3 2021

jwb committed rP567098: sysutils/slurm-wlm: More precise hdf5 dependency.
sysutils/slurm-wlm: More precise hdf5 dependency
Mar 3 2021, 4:30 PM

Feb 25 2021

jwb committed rP566566: auto-admin: Update to 0.7.0.9.
auto-admin: Update to 0.7.0.9
Feb 25 2021, 10:07 PM

Feb 14 2021

jwb committed rP565257: lang/pocl: Reverse broken RUN_DEPENDS change from last commit.
lang/pocl: Reverse broken RUN_DEPENDS change from last commit
Feb 14 2021, 6:07 PM
jwb committed rP565230: sysutils/auto-admin: Update to 0.7.0.3.
sysutils/auto-admin: Update to 0.7.0.3
Feb 14 2021, 2:43 PM
jwb committed rP565224: lang/pocl: Update hwloc dependency to hwloc2.
lang/pocl: Update hwloc dependency to hwloc2
Feb 14 2021, 1:04 PM

Feb 7 2021

jwb committed rP564637: sysutils/spcm: Update to 0.5.3.
sysutils/spcm: Update to 0.5.3
Feb 7 2021, 7:25 PM
jwb committed rP564636: sysutils/desktop-installer: Update to 0.7.0.
sysutils/desktop-installer: Update to 0.7.0
Feb 7 2021, 7:24 PM
jwb committed rP564635: sysutils/auto-admin: Update to 0.7.0.
sysutils/auto-admin: Update to 0.7.0
Feb 7 2021, 7:23 PM

Feb 5 2021

jwb committed rP564072: biology/py-multiqc: Update to 1.9.
biology/py-multiqc: Update to 1.9
Feb 5 2021, 1:37 AM

Feb 4 2021

jwb committed rP564040: biology/fastqc: Update to 0.11.9.
biology/fastqc: Update to 0.11.9
Feb 4 2021, 3:56 PM

Feb 2 2021

jwb committed rP563844: biology/py-cutadapt: Update to 3.2.
biology/py-cutadapt: Update to 3.2
Feb 2 2021, 8:39 PM

Jan 30 2021

jwb committed rP563428: biology/bowtie2: Reverse switch to devel/onetbb.
biology/bowtie2: Reverse switch to devel/onetbb
Jan 30 2021, 5:44 PM
jwb committed rP563427: biology/bowtie2: Switch to devel/onetbb.
biology/bowtie2: Switch to devel/onetbb
Jan 30 2021, 5:40 PM
jwb committed rP563418: biology/vsearch: Update to 2.15.2.
biology/vsearch: Update to 2.15.2
Jan 30 2021, 3:31 PM

Jan 29 2021

jwb committed rP563261: sysutils/spcm: Update to 0.5.2.
sysutils/spcm: Update to 0.5.2
Jan 29 2021, 11:09 PM
jwb committed rP563260: sysutils/auto-admin: Update to 0.6.12.
sysutils/auto-admin: Update to 0.6.12
Jan 29 2021, 10:53 PM

Jan 26 2021

jwb committed rP562629: sysutils/slurm-wlm: Patch to work with hdf5 1.12.
sysutils/slurm-wlm: Patch to work with hdf5 1.12
Jan 26 2021, 2:23 AM
jwb committed rP562627: biology/kallisto: Add -lz for pending hdf5 upgrade.
biology/kallisto: Add -lz for pending hdf5 upgrade
Jan 26 2021, 1:34 AM

Jan 24 2021

jwb committed rP562501: biology/bedtools: Upgrade to 2.30.0.
biology/bedtools: Upgrade to 2.30.0
Jan 24 2021, 6:25 PM

Jan 23 2021

jwb committed rP562414: biology/haplohseq: Fix example scripts for python 3.
biology/haplohseq: Fix example scripts for python 3
Jan 23 2021, 7:32 PM

Jan 22 2021

jwb committed rP562312: biology/bedtools: License changed upstream.
biology/bedtools: License changed upstream
Jan 22 2021, 2:55 PM

Jan 15 2021

jwb committed rP561615: biology/haplohseq: Restrict to python3.
biology/haplohseq: Restrict to python3
Jan 15 2021, 2:41 AM

Jan 14 2021

jwb committed rP561567: biology/haplohseq: Resurrect and fix python2 dependency.
biology/haplohseq: Resurrect and fix python2 dependency
Jan 14 2021, 3:52 PM

Jan 13 2021

jwb committed rP561514: sysutils/spcm: Update to 0.5.1.1.
sysutils/spcm: Update to 0.5.1.1
Jan 13 2021, 10:12 PM
jwb committed rP561513: sysutils/desktop-installer: Update to 0.6.20.3.
sysutils/desktop-installer: Update to 0.6.20.3
Jan 13 2021, 10:09 PM
jwb committed rP561511: sysutils/auto-admin: Update to 0.6.11.4.
sysutils/auto-admin: Update to 0.6.11.4
Jan 13 2021, 10:05 PM
jwb committed rP561488: sysutils/spcm: Update to 0.5.1.
sysutils/spcm: Update to 0.5.1
Jan 13 2021, 4:33 PM

Jan 11 2021

jwb committed rP561262: math/mprime: Switch from hwloc to hwloc2.
math/mprime: Switch from hwloc to hwloc2
Jan 11 2021, 8:26 PM
jwb committed rP561235: biology/star: Drop dependency on gcc.
biology/star: Drop dependency on gcc
Jan 11 2021, 5:45 PM
jwb committed rP561236: sysutils/parafly: Upgrade to 0.1.0 from Github, drop gcc dependency.
sysutils/parafly: Upgrade to 0.1.0 from Github, drop gcc dependency
Jan 11 2021, 5:45 PM
jwb committed rP561233: biology/ncbi-blast+: Drop dependency on gcc.
biology/ncbi-blast+: Drop dependency on gcc
Jan 11 2021, 5:45 PM
jwb committed rP561234: biology/stacks: Drop dependency on gcc.
biology/stacks: Drop dependency on gcc
Jan 11 2021, 5:45 PM
jwb committed rP561231: biology/gcta: Drop dependency on gcc.
biology/gcta: Drop dependency on gcc
Jan 11 2021, 5:45 PM
jwb committed rP561229: biology/fasttree: Drop dependency on gcc.
biology/fasttree: Drop dependency on gcc
Jan 11 2021, 5:45 PM
jwb committed rP561228: biology/cd-hit: Drop dependency on gcc.
biology/cd-hit: Drop dependency on gcc
Jan 11 2021, 5:45 PM
jwb committed rP561227: biology/canu: Drop dependency on gcc.
biology/canu: Drop dependency on gcc
Jan 11 2021, 5:45 PM

Jan 8 2021

jwb committed rP560817: biology/pooler: Upgrade to 1.76.
biology/pooler: Upgrade to 1.76
Jan 8 2021, 10:44 PM
jwb committed rP560811: net/aluminum: Upgrade hwloc dep to hwloc2.
net/aluminum: Upgrade hwloc dep to hwloc2
Jan 8 2021, 8:46 PM
jwb committed rP560810: science/gromacs: Upgrade hwloc dep to hwloc2.
science/gromacs: Upgrade hwloc dep to hwloc2
Jan 8 2021, 8:44 PM
jwb committed rP560809: devel/hpx: Upgrade hwloc dep to hwloc2.
devel/hpx: Upgrade hwloc dep to hwloc2
Jan 8 2021, 8:42 PM

Jan 7 2021

jwb committed rP560733: sysutils/slurm-wlm: Switch from hwloc to hwloc2.
sysutils/slurm-wlm: Switch from hwloc to hwloc2
Jan 7 2021, 8:32 PM

Jan 6 2021

jwb committed rP560522: sysutils/desktop-installer: Update to 0.6.20.
sysutils/desktop-installer: Update to 0.6.20
Jan 6 2021, 2:21 PM
jwb committed rP560515: sysutils/spcm: Tools for building and managing HPC clusters.
sysutils/spcm: Tools for building and managing HPC clusters
Jan 6 2021, 1:57 PM
jwb committed rP560513: sysutils/auto-admin: Update to 0.6.11.
sysutils/auto-admin: Update to 0.6.11
Jan 6 2021, 1:46 PM

Jan 2 2021

jwb committed rP559975: biology/gemma: Upgrade to 0.98.3.
biology/gemma: Upgrade to 0.98.3
Jan 2 2021, 10:06 PM

Dec 27 2020

jwb committed rP559434: sysutils/desktop-installer: Update to 0.6.19.
sysutils/desktop-installer: Update to 0.6.19
Dec 27 2020, 10:49 PM
jwb committed rP559433: sysutils/auto-admin: Update to 0.6.10.
sysutils/auto-admin: Update to 0.6.10
Dec 27 2020, 10:43 PM

Dec 17 2020

jwb committed rP558304: sysutils/auto-admin: Upgrade to 0.6.9.
sysutils/auto-admin: Upgrade to 0.6.9
Dec 17 2020, 4:44 PM

Dec 9 2020

jwb committed rP557373: MFH: r556796 r557295.
MFH: r556796 r557295
Dec 9 2020, 1:45 PM

Dec 8 2020

jwb committed rP557295: sysutils/slurm-wlm: Back out -fno-common patches, add -fcommon flag.
sysutils/slurm-wlm: Back out -fno-common patches, add -fcommon flag
Dec 8 2020, 4:21 PM

Dec 1 2020

jwb committed rP556796: sysutils/slurm-wlm: Patch in lua 5.4 support.
sysutils/slurm-wlm: Patch in lua 5.4 support
Dec 1 2020, 10:03 PM

Nov 16 2020

jwb committed rP555505: biology/ncbi-blast+: Upgrade to 2.11.0.
biology/ncbi-blast+: Upgrade to 2.11.0
Nov 16 2020, 6:25 PM

Nov 15 2020

jwb committed rP555418: biology/pooler: Optimise DNA sequencing primer-set combinations.
biology/pooler: Optimise DNA sequencing primer-set combinations
Nov 15 2020, 6:50 PM

Nov 9 2020

jwb committed rP554660: biology/vt: Fix build with htslib 1.11.
biology/vt: Fix build with htslib 1.11
Nov 9 2020, 12:36 AM

Nov 8 2020

jwb committed rP554467: biology/gcta: Switch eigen3 dep to USES framework.
biology/gcta: Switch eigen3 dep to USES framework
Nov 8 2020, 2:48 PM

Nov 7 2020

jwb committed rP554390: biology/bowtie2: Upgrade to 2.4.2.
biology/bowtie2: Upgrade to 2.4.2
Nov 7 2020, 1:47 PM

Nov 5 2020

jwb committed rP554157: biology/bcftools: Upgrade to 1.11.
biology/bcftools: Upgrade to 1.11
Nov 5 2020, 8:34 PM
jwb committed rP554156: biology/samtools: Upgrade to 1.11.
biology/samtools: Upgrade to 1.11
Nov 5 2020, 8:32 PM
jwb committed rP554155: biology/htslib: Upgrade to 1.11.0.
biology/htslib: Upgrade to 1.11.0
Nov 5 2020, 8:31 PM

Nov 3 2020

jwb committed rP554012: devel/py-srsly: Upgrade to 2.3.1.
devel/py-srsly: Upgrade to 2.3.1
Nov 3 2020, 7:09 PM

Oct 30 2020

jwb committed rP553694: sysutils/desktop-installer: Upgrade to 0.6.18.
sysutils/desktop-installer: Upgrade to 0.6.18
Oct 30 2020, 2:56 PM
jwb committed rP553689: sysutils/auto-admin: Upgrade to 0.6.8.
sysutils/auto-admin: Upgrade to 0.6.8
Oct 30 2020, 1:34 PM

Oct 16 2020

jwb committed rP552519: biology/py-biopython: Upgrade to 1.78.
biology/py-biopython: Upgrade to 1.78
Oct 16 2020, 7:13 PM

Oct 1 2020

jwb committed rP550854: sysutils/ganglia-monitor-core: Upgrade to 3.7.2, disable python modules.
sysutils/ganglia-monitor-core: Upgrade to 3.7.2, disable python modules
Oct 1 2020, 6:01 PM

Sep 22 2020

jwb committed rP549546: biology/gmap: Upgrade to 2020.09.12.
biology/gmap: Upgrade to 2020.09.12
Sep 22 2020, 12:56 AM

Sep 18 2020

jwb committed rP548871: biology/subread: Add -fcommon for clang 11.
biology/subread: Add -fcommon for clang 11
Sep 18 2020, 12:57 AM

Sep 14 2020

jwb committed rP548685: biology/canu: Upgrade to 2.1.
biology/canu: Upgrade to 2.1
Sep 14 2020, 10:27 PM

Aug 30 2020

jwb committed rP547056: biology/picard-tools: Remove extraneous file.
biology/picard-tools: Remove extraneous file
Aug 30 2020, 2:07 PM

Aug 11 2020

jwb committed rP544688: MFH: r544687.
MFH: r544687
Aug 11 2020, 3:34 PM
jwb committed rP544687: sysutils/auto-admin: Upgrade to 0.6.7 bugfix release.
sysutils/auto-admin: Upgrade to 0.6.7 bugfix release
Aug 11 2020, 3:02 PM

Aug 3 2020

jwb committed rP544098: biology/samtools: Upgrade to 1.10.
biology/samtools: Upgrade to 1.10
Aug 3 2020, 6:22 PM
jwb committed rP544096: biology/bcftools: Upgrade to 1.10.2.
biology/bcftools: Upgrade to 1.10.2
Aug 3 2020, 6:17 PM