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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 (208 w, 4 d)

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

Recent Activity

Yesterday

jwb committed R11:d8bc1eb7963a: biology/hisat2: Update to 2.2.1 (authored by jwb).
biology/hisat2: Update to 2.2.1
Fri, Nov 26, 10:07 PM
jwb committed R11:869afa4fe605: biology/star: Update to 2.7.9a (authored by jwb).
biology/star: Update to 2.7.9a
Fri, Nov 26, 9:59 PM

Wed, Nov 10

jwb committed R11:17f3e2cbe6f1: biostar-tools: Add gffread to metaport deps (authored by jwb).
biostar-tools: Add gffread to metaport deps
Wed, Nov 10, 8:54 PM
jwb committed R11:8d2198bb6d6b: biology/gffread: GFF/GTF format conversions, filtering, FASTA extraction, etc (authored by jwb).
biology/gffread: GFF/GTF format conversions, filtering, FASTA extraction, etc
Wed, Nov 10, 8:51 PM
jwb committed R11:ab8b8cfa4f87: sysutils/desktop-installer: Update to 0.7.5.4 (authored by jwb).
sysutils/desktop-installer: Update to 0.7.5.4
Wed, Nov 10, 3:36 PM
jwb committed R11:8ab1850c3e5c: sysutils/auto-admin: Update to 0.7.7 (authored by jwb).
sysutils/auto-admin: Update to 0.7.7
Wed, Nov 10, 3:29 PM

Sat, Nov 6

jwb committed R11:e95d561eab5d: sysutils/spcm: Update to 0.5.4.9 (authored by jwb).
sysutils/spcm: Update to 0.5.4.9
Sat, Nov 6, 1:42 AM

Thu, Nov 4

jwb committed R11:e02229c22ccb: biology/vcflib: Update to 1.0.2 (authored by jwb).
biology/vcflib: Update to 1.0.2
Thu, Nov 4, 2:28 PM

Wed, Nov 3

jwb committed R11:dc64b13129b8: biology/freebayes: Update to 1.3.5 (authored by jwb).
biology/freebayes: Update to 1.3.5
Wed, Nov 3, 8:54 PM

Sat, Oct 30

jwb committed R11:4df7493e1004: biology/biostar-tools: Add biology/igv to metaport deps (authored by jwb).
biology/biostar-tools: Add biology/igv to metaport deps
Sat, Oct 30, 3:29 PM

Oct 20 2021

jwb committed R11:9636d7ad40ff: biology/bamutil: Update to 1.0.15 (authored by jwb).
biology/bamutil: Update to 1.0.15
Oct 20 2021, 7:45 PM
jwb committed R11:f6c6c5a37954: biology/fastp: Update to 0.23.1 (authored by jwb).
biology/fastp: Update to 0.23.1
Oct 20 2021, 4:38 PM

Oct 14 2021

jwb committed R11:9d1d409f4253: biology/biostar-tools: Add py-deeptools to metaport deps (authored by jwb).
biology/biostar-tools: Add py-deeptools to metaport deps
Oct 14 2021, 11:57 AM
jwb committed R11:799d4cc2cfd1: biology/py-deeptools: User-friendly tools for exploring deep-sequencing data (authored by jwb).
biology/py-deeptools: User-friendly tools for exploring deep-sequencing data
Oct 14 2021, 11:54 AM

Oct 13 2021

jwb committed R11:ad5a0604c41c: biology/py-bigwig: Rename to biology/py-pybigwig (authored by jwb).
biology/py-bigwig: Rename to biology/py-pybigwig
Oct 13 2021, 9:27 PM
jwb committed R11:06e26353b27a: biology/py-deeptoolsintervals: Python interface for deepTools interval trees (authored by jwb).
biology/py-deeptoolsintervals: Python interface for deepTools interval trees
Oct 13 2021, 4:05 PM
jwb committed R11:646f3fc38189: biology/py-py-pybigwig: Patch out setup.py warning (authored by jwb).
biology/py-py-pybigwig: Patch out setup.py warning
Oct 13 2021, 4:05 PM
jwb committed R11:c69e97e63ac3: biology/py-pybigwig: Fix poudriere build (authored by jwb).
biology/py-pybigwig: Fix poudriere build
Oct 13 2021, 4:05 PM
jwb committed R11:904a889fd144: biology/py-pybigwig: Python access to bigWig files using libBigWig (authored by jwb).
biology/py-pybigwig: Python access to bigWig files using libBigWig
Oct 13 2021, 1:06 PM
jwb committed R11:d92344039b43: biology/py-py2bit: Python interface for 2bit packed nucleotide files (authored by jwb).
biology/py-py2bit: Python interface for 2bit packed nucleotide files
Oct 13 2021, 12:56 PM

Oct 12 2021

jwb committed R11:2e8996e43d71: biology/biostar-tools: Add biology/bamutil to metaport deps (authored by jwb).
biology/biostar-tools: Add biology/bamutil to metaport deps
Oct 12 2021, 4:46 PM
jwb committed R11:cdf2ff2f68e6: biology/bamutil: Utilities for working with SAM/BAM files (authored by jwb).
biology/bamutil: Utilities for working with SAM/BAM files
Oct 12 2021, 4:43 PM

Sep 27 2021

jwb committed R11:96d32d811873: biology/biostar-tools: Add biology/kallisto run depend to metaport (authored by jwb).
biology/biostar-tools: Add biology/kallisto run depend to metaport
Sep 27 2021, 12:17 PM

Sep 24 2021

jwb committed R11:d94f19ab9ffc: biology/ucsc-userapps: Add "kent" command in ${PREFIX}/bin (authored by jwb).
biology/ucsc-userapps: Add "kent" command in ${PREFIX}/bin
Sep 24 2021, 9:58 PM
jwb committed R11:c68b6dc6448c: biology/emboss: Add "emboss" command in ${LOCALBASE}/bin (authored by jwb).
biology/emboss: Add "emboss" command in ${LOCALBASE}/bin
Sep 24 2021, 9:39 PM

Sep 20 2021

jwb committed R11:d157b2969c9f: sysutils/spcm: Update to 0.5.4.4 (authored by jwb).
sysutils/spcm: Update to 0.5.4.4
Sep 20 2021, 2:38 PM

Sep 17 2021

jwb accepted D31984: biology/jellyfish: Fix build when NLS knob is off.

Looks good, thanks!

Sep 17 2021, 5:39 PM
jwb committed R11:4489fc44b267: devel/libxtend: Update to 0.1.3.5 (authored by jwb).
devel/libxtend: Update to 0.1.3.5
Sep 17 2021, 4:39 PM
jwb committed R11:623975bcb451: biology/biolibc: Update to 0.2.0.11 (authored by jwb).
biology/biolibc: Update to 0.2.0.11
Sep 17 2021, 4:36 PM
jwb added a comment to D31984: biology/jellyfish: Fix build when NLS knob is off.

Interesting. I've personally never been hit by a Github tarball reroll, so I'm not too concerned. I'll commit without the static tarball change for now and investigate this further when I can make some time for proper regression testing.

Sep 17 2021, 1:05 PM
jwb added a comment to D31984: biology/jellyfish: Fix build when NLS knob is off.

Thanks for the heads-up. I'm not inclined to trust a hand-rolled distfile when the only benefit is avoiding an autoreconf, though. I'll commit the NLS and license changes ASAP.

Sep 17 2021, 12:40 PM

Sep 15 2021

jwb committed R11:394e4d5fdb60: sysutils/auto-admin: Update to 0.7.6.11 (authored by jwb).
sysutils/auto-admin: Update to 0.7.6.11
Sep 15 2021, 1:45 PM

Sep 11 2021

jwb committed R11:696f6acf5df4: biology/jellyfish: Fix unused open mode variable (authored by jwb).
biology/jellyfish: Fix unused open mode variable
Sep 11 2021, 12:32 PM

Sep 10 2021

jwb committed R11:8309dd7c64f5: sysutils/desktop-installer: Update to 0.7.5 (authored by jwb).
sysutils/desktop-installer: Update to 0.7.5
Sep 10 2021, 2:29 PM
jwb committed R11:3ce991a5e158: sysutils/auto-admin: Update to 0.7.6 (authored by jwb).
sysutils/auto-admin: Update to 0.7.6
Sep 10 2021, 2:27 PM

Sep 7 2021

jwb committed R11:c73e3a89ec72: biology/biostar-tools: Add biology/sam2pairwise to run deps (authored by jwb).
biology/biostar-tools: Add biology/sam2pairwise to run deps
Sep 7 2021, 8:43 PM
jwb committed R11:e61df5e46475: biology/sam2pairwise: Show pairwise alignment for each read in a SAM file (authored by jwb).
biology/sam2pairwise: Show pairwise alignment for each read in a SAM file
Sep 7 2021, 8:34 PM

Sep 6 2021

jwb committed R11:e47c577da6ce: biology/emboss: Put emboss-shell in default PATH (authored by jwb).
biology/emboss: Put emboss-shell in default PATH
Sep 6 2021, 3:17 PM
jwb committed R11:0ec8be4158ca: biology/biostar-tools: Add mafft, clustal-omega, pywgsim deps (authored by jwb).
biology/biostar-tools: Add mafft, clustal-omega, pywgsim deps
Sep 6 2021, 2:29 PM
jwb committed R11:fa2e0b8c66d4: biology/emboss: Add emboss-shell: Run subshell with proper PATH (authored by jwb).
biology/emboss: Add emboss-shell: Run subshell with proper PATH
Sep 6 2021, 2:24 PM
jwb committed R11:c085af1e8147: biology/py-pywgsim: Modified wgsim genomic data simulator (authored by jwb).
biology/py-pywgsim: Modified wgsim genomic data simulator
Sep 6 2021, 12:56 PM

Sep 2 2021

jwb committed R11:7e94c6d1f86c: biology/peak-classifier: Update to 0.1.1.21 (authored by jwb).
biology/peak-classifier: Update to 0.1.1.21
Sep 2 2021, 11:16 PM
jwb committed R11:df5931308708: biology/biolibc: Update to 0.2.0.1 (authored by jwb).
biology/biolibc: Update to 0.2.0.1
Sep 2 2021, 11:14 PM

Aug 31 2021

jwb committed R11:9e8689607ec9: Mk/bsd.local.mk: Remove accidentally committed local mods (authored by jwb).
Mk/bsd.local.mk: Remove accidentally committed local mods
Aug 31 2021, 2:05 PM
jwb committed R11:5a521ba8f868: x11/coreterminal: Terminal emulator from the CoreApps family (authored by jwb).
x11/coreterminal: Terminal emulator from the CoreApps family
Aug 31 2021, 1:35 PM
jwb committed R11:73855f4916c2: coregarage: Remove extraneous portrevision (authored by jwb).
coregarage: Remove extraneous portrevision
Aug 31 2021, 1:30 PM
jwb committed R11:e562107239ac: deskutils/coregarage: Settings manager for C Suite (authored by jwb).
deskutils/coregarage: Settings manager for C Suite
Aug 31 2021, 1:28 PM
jwb committed R11:6f4cee7a82a2: deskutils/libcprime: Bookmarking, saving activites, managing settings (authored by jwb).
deskutils/libcprime: Bookmarking, saving activites, managing settings
Aug 31 2021, 1:25 PM
jwb committed R11:9c7c5e9cfa4e: archivers/libarchive-qt: Qt based archiving with libarchive backend (authored by jwb).
archivers/libarchive-qt: Qt based archiving with libarchive backend
Aug 31 2021, 1:15 PM

Aug 30 2021

jwb committed R11:904aa6046960: biology/biolibc-tools: High-performance tools based on biolibc (authored by jwb).
biology/biolibc-tools: High-performance tools based on biolibc
Aug 30 2021, 1:10 PM

Aug 28 2021

jwb committed R11:541454f9939d: biology/pooler: Update to 1.78 (authored by jwb).
biology/pooler: Update to 1.78
Aug 28 2021, 2:38 PM
jwb committed R11:b16616b283a7: biology/peak-classifier: Update to 0.1.1.20 (authored by jwb).
biology/peak-classifier: Update to 0.1.1.20
Aug 28 2021, 1:36 AM
jwb committed R11:dc651f0234fb: biology/vcf2hap: Update to 0.1.3.12 (authored by jwb).
biology/vcf2hap: Update to 0.1.3.12
Aug 28 2021, 1:36 AM
jwb committed R11:61ebfe4137ea: biology/vcf-split: Update to 0.1.2.14 (authored by jwb).
biology/vcf-split: Update to 0.1.2.14
Aug 28 2021, 1:36 AM
jwb committed R11:b30b9f1a1ec8: biology/ad2vcf: Update to 0.1.3.31 (authored by jwb).
biology/ad2vcf: Update to 0.1.3.31
Aug 28 2021, 1:36 AM
jwb committed R11:9876430959ae: biology/biolibc: Update to 0.2.0 (authored by jwb).
biology/biolibc: Update to 0.2.0
Aug 28 2021, 1:36 AM
jwb committed R11:3367ccebd29c: devel/libxtend: Update to 0.1.3.1 (authored by jwb).
devel/libxtend: Update to 0.1.3.1
Aug 28 2021, 1:36 AM

Aug 26 2021

jwb committed R11:7813a6f1a164: biology/fastp: Update to 0.22.0 (authored by jwb).
biology/fastp: Update to 0.22.0
Aug 26 2021, 7:49 PM

Aug 24 2021

jwb committed R11:1e0d8ce2079e: biostar-tools: Update to 1.4.0 (authored by jwb).
biostar-tools: Update to 1.4.0
Aug 24 2021, 4:48 PM

Aug 23 2021

jwb committed R11:2e559ca48c93: biology/bfc: Correct sequencing errors from Illumina sequencing data (authored by jwb).
biology/bfc: Correct sequencing errors from Illumina sequencing data
Aug 23 2021, 5:29 PM
jwb committed R11:615c521bb3a0: biology/flash: Fast Length Adjustment of SHort reads (authored by jwb).
biology/flash: Fast Length Adjustment of SHort reads
Aug 23 2021, 5:28 PM

Aug 22 2021

jwb committed R11:d09fdd5d58f4: biology/minimap2: Add pkg-plist to repo (authored by jwb).
biology/minimap2: Add pkg-plist to repo
Aug 22 2021, 5:48 PM
jwb committed R11:4952cf637ae5: biology/jellyfish: Update to 2.3.0 (authored by jwb).
biology/jellyfish: Update to 2.3.0
Aug 22 2021, 5:45 PM
jwb committed R11:205fcac2210b: biology/minimap2: Update to 2.22 (authored by jwb).
biology/minimap2: Update to 2.22
Aug 22 2021, 2:17 PM
jwb committed R11:c5efaea23b87: biology/bbmap: Update to 38.92 (authored by jwb).
biology/bbmap: Update to 38.92
Aug 22 2021, 2:01 PM

Aug 21 2021

jwb committed R11:472c25aa5d8d: biology/pooler: Update to 1.77 (authored by jwb).
biology/pooler: Update to 1.77
Aug 21 2021, 10:13 PM

Aug 13 2021

jwb committed R11:361278dd7c67: biostar-tools: Correct category for py-ont-fast5-api (authored by jwb).
biostar-tools: Correct category for py-ont-fast5-api
Aug 13 2021, 2:17 PM
jwb committed R11:3ed2dd540f07: biostar-tools: Add new deps to metaport (authored by jwb).
biostar-tools: Add new deps to metaport
Aug 13 2021, 1:39 PM
jwb committed R11:5797d6a3298e: biology/py-ont-fast5-api: Interface to Oxford Nanopore .fast5 files (authored by jwb).
biology/py-ont-fast5-api: Interface to Oxford Nanopore .fast5 files
Aug 13 2021, 1:35 PM
jwb committed R11:35f24e09c672: archivers/vbz-compression: Compression for Oxford Nanopore signal data (authored by jwb).
archivers/vbz-compression: Compression for Oxford Nanopore signal data
Aug 13 2021, 1:50 AM
jwb committed R11:ebe45fb054f9: archivers/streamvbyte: Integer compression with SIMD based on Google's varint (authored by jwb).
archivers/streamvbyte: Integer compression with SIMD based on Google's varint
Aug 13 2021, 12:39 AM

Jul 12 2021

jwb committed R11:94c639f5ff16: biology/bcftools: Update to 1.13 (authored by jwb).
biology/bcftools: Update to 1.13
Jul 12 2021, 1:38 PM
jwb committed R11:1c1b4943aef7: biology/samtools: Update to 1.13 (authored by jwb).
biology/samtools: Update to 1.13
Jul 12 2021, 1:38 PM
jwb committed R11:5fa07128ec66: htslib: Update to 1.13 (authored by jwb).
htslib: Update to 1.13
Jul 12 2021, 1:38 PM

Jul 9 2021

jwb committed R11:abcde3081443: biology/biostar-tools: Add erminej run depend to metaport (authored by jwb).
biology/biostar-tools: Add erminej run depend to metaport
Jul 9 2021, 12:37 PM
jwb committed R11:e44f917e298a: biology/erminej: Analyses of gene sets, e.g. gene expression profiling (authored by jwb).
biology/erminej: Analyses of gene sets, e.g. gene expression profiling
Jul 9 2021, 12:29 PM

Jul 6 2021

jwb committed R11:814a894e9012: biology/bamtools: Update to 2.5.2 (authored by jwb).
biology/bamtools: Update to 2.5.2
Jul 6 2021, 6:13 PM

Jul 2 2021

jwb committed R11:8b48d38ecee3: biology/biostar-tools: Add biology/py-goatools to metaport depends (authored by jwb).
biology/biostar-tools: Add biology/py-goatools to metaport depends
Jul 2 2021, 5:04 PM
jwb committed R11:7fd4d4420f37: biology/py-goatools: Tools for processing and visualizing Gene Ontology terms (authored by jwb).
biology/py-goatools: Tools for processing and visualizing Gene Ontology terms
Jul 2 2021, 5:01 PM
jwb committed R11:e35c0e08648a: biology/ncbi-blast+: Update to 2.12.0 (authored by jwb).
biology/ncbi-blast+: Update to 2.12.0
Jul 2 2021, 4:48 PM

Jun 29 2021

jwb committed R11:a881e9d0c3cc: biology/mmseqs2: Fix runtime error when built with clang (authored by jwb).
biology/mmseqs2: Fix runtime error when built with clang
Jun 29 2021, 2:10 PM

Jun 28 2021

jwb committed R11:ded91b5047b0: sysutils/desktop-installer: Update to 0.7.4.5 (authored by jwb).
sysutils/desktop-installer: Update to 0.7.4.5
Jun 28 2021, 12:52 PM
jwb committed R11:c5fe54159563: sysutils/auto-admin: Update to 0.7.5.5 (authored by jwb).
sysutils/auto-admin: Update to 0.7.5.5
Jun 28 2021, 12:43 PM
jwb committed R11:97f088e86852: biology/biostar-tools: Remove falsehood in pkg-message (authored by jwb).
biology/biostar-tools: Remove falsehood in pkg-message
Jun 28 2021, 12:03 AM

Jun 26 2021

jwb committed R11:b8bf1cfd41e7: biology/mmseqs2: Enable at least SSE2 by default (authored by jwb).
biology/mmseqs2: Enable at least SSE2 by default
Jun 26 2021, 4:31 PM

Jun 24 2021

jwb committed R11:287eab190236: sysutils/slurm-wlm: Update to 20.02.7 (authored by jwb).
sysutils/slurm-wlm: Update to 20.02.7
Jun 24 2021, 9:58 PM
jwb committed R11:cf14bbb325bb: biology/mmseqs2: Ultra fast and sensitive sequence search and clustering suite (authored by jwb).
biology/mmseqs2: Ultra fast and sensitive sequence search and clustering suite
Jun 24 2021, 5:32 PM

Jun 22 2021

jwb committed R11:1885ed0eb124: biostar-tools: Add sra-tools dependency to metaport (authored by jwb).
biostar-tools: Add sra-tools dependency to metaport
Jun 22 2021, 6:01 PM
jwb committed R11:69656bf0d7d9: biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read… (authored by jwb).
biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read…
Jun 22 2021, 5:58 PM

Jun 21 2021

jwb committed R11:65490b0eb586: sysutils/auto-admin: Update to 0.7.5.2 (authored by jwb).
sysutils/auto-admin: Update to 0.7.5.2
Jun 21 2021, 7:08 PM

Jun 19 2021

jwb committed R11:d571f1f33222: biology/vsearch: Update to 2.17.1 (authored by jwb).
biology/vsearch: Update to 2.17.1
Jun 19 2021, 12:35 PM

Jun 18 2021

jwb committed R11:6df92a09ad7a: biology/biostar-tools: Meta-port for Biostar Handbook tools (authored by jwb).
biology/biostar-tools: Meta-port for Biostar Handbook tools
Jun 18 2021, 9:57 PM
jwb committed R11:98807e08be7e: science/csvtk: Cross-platform and ultrafast toolkit for CSV/TSV processing (authored by jwb).
science/csvtk: Cross-platform and ultrafast toolkit for CSV/TSV processing
Jun 18 2021, 9:29 PM

Jun 17 2021

jwb committed R11:0b83e8dde93c: benchmarks/mst-bench: Maximum sustainable throughput benchmark (authored by jwb).
benchmarks/mst-bench: Maximum sustainable throughput benchmark
Jun 17 2021, 5:07 PM

Jun 16 2021

jwb committed R11:2d2482b02a33: sysutils/desktop-installer: Update to 0.7.4 (authored by jwb).
sysutils/desktop-installer: Update to 0.7.4
Jun 16 2021, 10:05 PM
jwb committed R11:cd778aa0e747: sysutils/auto-admin: Update to 0.7.5 (authored by jwb).
sysutils/auto-admin: Update to 0.7.5
Jun 16 2021, 9:05 PM

Jun 14 2021

jwb committed R11:5a2a6eb32954: biology/peak-classifier: Classify peaks based on GFF features (authored by jwb).
biology/peak-classifier: Classify peaks based on GFF features
Jun 14 2021, 4:42 PM

Jun 11 2021

jwb committed R11:46f77e921f4e: biology/vcf2hap: Remove comment used to silence portlint (authored by jwb).
biology/vcf2hap: Remove comment used to silence portlint
Jun 11 2021, 3:41 PM
jwb committed R11:c906bf342e2f: biology/ad2vcf: Remove comment used to silence portlint (authored by jwb).
biology/ad2vcf: Remove comment used to silence portlint
Jun 11 2021, 3:41 PM
jwb committed R11:e93f518118ec: devel/libxtend: Remove comment used to silence portlint (authored by jwb).
devel/libxtend: Remove comment used to silence portlint
Jun 11 2021, 3:41 PM