♟ jwb

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

biology/hisat2: Update to 2.2.1

biology/star: Update to 2.7.9a

biostar-tools: Add gffread to metaport deps

biology/gffread: GFF/GTF format conversions, filtering, FASTA extraction, etc

sysutils/desktop-installer: Update to 0.7.5.4

sysutils/auto-admin: Update to 0.7.7

sysutils/spcm: Update to 0.5.4.9

biology/vcflib: Update to 1.0.2

biology/freebayes: Update to 1.3.5

biology/biostar-tools: Add biology/igv to metaport deps

biology/bamutil: Update to 1.0.15

biology/fastp: Update to 0.23.1

biology/biostar-tools: Add py-deeptools to metaport deps

biology/py-deeptools: User-friendly tools for exploring deep-sequencing data

biology/py-bigwig: Rename to biology/py-pybigwig

biology/py-deeptoolsintervals: Python interface for deepTools interval trees

biology/py-py-pybigwig: Patch out setup.py warning

biology/py-pybigwig: Fix poudriere build

biology/py-pybigwig: Python access to bigWig files using libBigWig

biology/py-py2bit: Python interface for 2bit packed nucleotide files

biology/biostar-tools: Add biology/bamutil to metaport deps

biology/bamutil: Utilities for working with SAM/BAM files

biology/biostar-tools: Add biology/kallisto run depend to metaport

biology/ucsc-userapps: Add "kent" command in ${PREFIX}/bin

biology/emboss: Add "emboss" command in ${LOCALBASE}/bin

sysutils/spcm: Update to 0.5.4.4

devel/libxtend: Update to 0.1.3.5

biology/biolibc: Update to 0.2.0.11

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.

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.

sysutils/auto-admin: Update to 0.7.6.11

biology/jellyfish: Fix unused open mode variable

sysutils/desktop-installer: Update to 0.7.5

sysutils/auto-admin: Update to 0.7.6

biology/biostar-tools: Add biology/sam2pairwise to run deps

biology/sam2pairwise: Show pairwise alignment for each read in a SAM file

biology/emboss: Put emboss-shell in default PATH

biology/biostar-tools: Add mafft, clustal-omega, pywgsim deps

biology/emboss: Add emboss-shell: Run subshell with proper PATH

biology/py-pywgsim: Modified wgsim genomic data simulator

biology/peak-classifier: Update to 0.1.1.21

biology/biolibc: Update to 0.2.0.1

Mk/bsd.local.mk: Remove accidentally committed local mods

x11/coreterminal: Terminal emulator from the CoreApps family

coregarage: Remove extraneous portrevision

deskutils/coregarage: Settings manager for C Suite

deskutils/libcprime: Bookmarking, saving activites, managing settings

archivers/libarchive-qt: Qt based archiving with libarchive backend

biology/biolibc-tools: High-performance tools based on biolibc

biology/pooler: Update to 1.78

biology/peak-classifier: Update to 0.1.1.20

biology/vcf2hap: Update to 0.1.3.12

biology/vcf-split: Update to 0.1.2.14

biology/ad2vcf: Update to 0.1.3.31

biology/biolibc: Update to 0.2.0

devel/libxtend: Update to 0.1.3.1

biology/fastp: Update to 0.22.0

biostar-tools: Update to 1.4.0

biology/bfc: Correct sequencing errors from Illumina sequencing data

biology/flash: Fast Length Adjustment of SHort reads

biology/minimap2: Add pkg-plist to repo

biology/jellyfish: Update to 2.3.0

biology/minimap2: Update to 2.22

biology/bbmap: Update to 38.92

biology/pooler: Update to 1.77

biostar-tools: Correct category for py-ont-fast5-api

biostar-tools: Add new deps to metaport

biology/py-ont-fast5-api: Interface to Oxford Nanopore .fast5 files

archivers/vbz-compression: Compression for Oxford Nanopore signal data

archivers/streamvbyte: Integer compression with SIMD based on Google's varint

biology/bcftools: Update to 1.13

biology/samtools: Update to 1.13

htslib: Update to 1.13

biology/biostar-tools: Add erminej run depend to metaport

biology/erminej: Analyses of gene sets, e.g. gene expression profiling

biology/bamtools: Update to 2.5.2

biology/biostar-tools: Add biology/py-goatools to metaport depends

biology/py-goatools: Tools for processing and visualizing Gene Ontology terms

biology/ncbi-blast+: Update to 2.12.0

biology/mmseqs2: Fix runtime error when built with clang

sysutils/desktop-installer: Update to 0.7.4.5

sysutils/auto-admin: Update to 0.7.5.5

biology/biostar-tools: Remove falsehood in pkg-message

biology/mmseqs2: Enable at least SSE2 by default

sysutils/slurm-wlm: Update to 20.02.7

biology/mmseqs2: Ultra fast and sensitive sequence search and clustering suite

biostar-tools: Add sra-tools dependency to metaport

biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read…

sysutils/auto-admin: Update to 0.7.5.2

biology/vsearch: Update to 2.17.1

biology/biostar-tools: Meta-port for Biostar Handbook tools

science/csvtk: Cross-platform and ultrafast toolkit for CSV/TSV processing

benchmarks/mst-bench: Maximum sustainable throughput benchmark

sysutils/desktop-installer: Update to 0.7.4

sysutils/auto-admin: Update to 0.7.5

biology/peak-classifier: Classify peaks based on GFF features

biology/vcf2hap: Remove comment used to silence portlint

biology/ad2vcf: Remove comment used to silence portlint

devel/libxtend: Remove comment used to silence portlint

jwb (jwb@freebsd.org)HPC Systems Programmer

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jwb (jwb@freebsd.org)
HPC Systems Programmer

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