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Two new features

Two two features were added on 2020-05-30:
  1. Repology links - each port now has a link to repology.org. See issue 148 for details.
  2. Ports I maintain report - port maintainers can now subscribe to a daily report of commits to the ports they maintain. See Watch ports I maintain at Report Subscriptions. Details at issue 138
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Number of commits: 229 (showing only 100 on this page) 1 | 2 | 3  »  
Fri, 3 Jul 2020
[ 21:15 jwb ] Original commit 
py-srsly 2.1.0 devel files touched by this commit Modern high-performance serialization utilities for Python
devel/py-srsly: Add missing python version requirement

Requires python 3.6+

Reported by:    pkg-fallout
Mon, 29 Jun 2020
[ 15:38 jwb ] Original commit 
py-srsly 2.1.0 devel files touched by this commit Modern high-performance serialization utilities for Python
devel/py-srsly: Modern high-performance serialization utilities for Python

This package bundles some of the best Python serialization libraries into one
standalone package, with a high-level API that makes it easy to write code
that's correct across platforms and Pythons. This allows us to provide all the
serialization utilities we need in a single binary wheel. Currently supports
JSON, JSONL, MessagePack, Pickle and YAML.
Sat, 20 Jun 2020
[ 14:31 jwb ] Original commit 
vsearch 2.15.0 biology files touched by this commit Versatile open-source tool for metagenomics
biology/vsearch: Update to 2.15.0

Numerous minor enhancements
Sat, 13 Jun 2020
[ 13:54 jwb ] Original commit 
picard-tools 2.22.9 biology files touched by this commit CLI tools for manipulating high-throughput sequencing (HTS) data
biology/picard-tools: CLI tools for manipulating sequencing data

Picard is a set of command line tools for manipulating high-throughput
sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file
formats are defined in the Hts-specs repository.
[ 13:42 jwb ] Original commit 
py-biopython 1.77 biology files touched by this commit Collection of Python modules for bioinformatics
biology/py-biopython: Set python requirement to 3.6+

New requirement for v1.77 overlooked during upgrade
Thu, 11 Jun 2020
[ 16:41 jwb ] Original commit 
desktop-installer 0.6.16 sysutils files touched by this commit Quickly configure a FreeBSD desktop system
sysutils/desktop-installer: Update to 0.6.16

Add Fluxbox and IceWM window managers to the menu
Improve instructions for GPU setup
Minor bug fixes
[ 16:13 jwb ] Original commit 
auto-admin 0.6.5 sysutils files touched by this commit Portable tools for automating systems management
auto-admin: Greatly improved auto-gpu-setup

Factored code to ensure consistent results
Add nv driver option for old nVidia GPUs
Add no driver/DRM and "don't touch my config" options
Fri, 5 Jun 2020
[ 02:45 jwb ] Original commit 
bioawk 1.0.7 biology files touched by this commit BWK awk modified for biological data
biology/bioawk: BWK awk modified for biological data

Bioawk is an extension to Brian Kernighan's awk, adding the support of several
common biological data formats, including optionally gzip'ed BED, GFF, SAM,
VCF, FASTA/Q and TAB-delimited formats with column names. It also adds a few
built-in functions and an command line option to use TAB as the input/output
delimiter. When the new functionality is not used, bioawk is intended to behave
exactly the same as the original BWK awk.
[ 01:55 jwb ] Original commit 
subread 2.0.1 biology files touched by this commit High-performance read alignment, quantification and mutation discovery
biology/subread: Read alignment, quantification and mutation discovery

The Subread package comprises a suite of software programs for processing
next-gen sequencing read data including:

    Subread: a general-purpose read aligner
    Subjunc: a read aligner developed for aligning RNA-seq reads
    featureCounts: a software program developed for counting reads to genomic
    features such as genes, exons, promoters and genomic bins.
    Sublong: a long-read aligner that is designed based on seed-and-vote.
    exactSNP: discovers SNPs by testing signals against local background noise.
Thu, 4 Jun 2020
[ 18:28 jwb ] Original commit 
vt 0.57721 biology files touched by this commit Discovers short variants from Next Generation Sequencing data
bioloty/vt: Discovers short variants from Next Generation Sequencing data
Tue, 2 Jun 2020
[ 18:13 jwb ] Original commit 
desktop-installer 0.6.15 sysutils files touched by this commit Quickly configure a FreeBSD desktop system
sysutils/desktop-installer: Upgrade to 0.6.15

Add Window Maker support
Add user-guidance on hardware write cache and su+j
Move upstream to Github
Refactor and clean up code
[ 18:10 jwb ] Original commit 
auto-admin 0.6.4 sysutils files touched by this commit Portable tools for automating systems management
sysutils/auto-admin: Upgrade to 0.6.4

Add Scripts for toggling UFS su+j and hardware write cache
Add auto-set-conf-var, sysrc-like script for sysctl and loader.conf
Move upstream to Github
Fri, 29 May 2020
[ 02:03 jwb ] Original commit 
py-biopython 1.77 biology files touched by this commit Collection of Python modules for bioinformatics
biology/py-biopython: Upgrade to 1.77

Upstream support for python 3

PR:             ports/246763
Submitted by:   Mauricio Herrera Cuadra <mauricio@arareko.net>
Sun, 24 May 2020
[ 15:23 jwb ] Original commit 
py-dnaio 0.4.2 biology files touched by this commit Read and write FASTQ and FASTA
biology/py-dnaio: Upgrade to 0.4.2

Reported by:    portscout
[ 15:20 jwb ] Original commit 
R-cran-optparse 1.6.6 devel files touched by this commit Command line flag parser inspired by Python's optparse
R-cran-optparse: Upgrade to 1.6.6

Reported by:    portscout
Sat, 9 May 2020
[ 13:37 jwb ] Original commit 
desktop-installer 0.6.13 sysutils files touched by this commit Quickly configure a FreeBSD desktop system
sysutils/desktop-installer: Upgrade to 0.6.13

Add support for Cinnamon desktop
Add unsupported option for CDE (not secure, for hobbyists/nostalgia only)
Mon, 4 May 2020
[ 23:01 jwb ] Original commit 
plink 1.90.b6.17 biology files touched by this commit Whole genome association analysis toolset
biology/plink: Whole genome association analysis toolset

Reversed removal, commit r471892 2018/06/07
Upgraded to 1.90 beta 6.17

PR:             ports/243733
Submitted by:   mzaki@e-mail.ne.jp
Fri, 1 May 2020
[ 14:31 jwb ] Original commit 
desktop-installer 0.6.12 sysutils files touched by this commit Quickly configure a FreeBSD desktop system
sysutils/desktop-installer: Upgrade to 0.6.12

Add option to enable Xorg SWCursor
Add XFCE4 + SLiM option
Other fixes, enhancements and clean-up
[ 14:25 jwb ] Original commit 
auto-admin 0.6.2 sysutils files touched by this commit Portable tools for automating systems management
sysutils/auto-admin: Upgrade to 0.6.2

New tools for keeping quarterly/head ports branch and pkg repo in sync
New tools for remote IPMI power-on and status
Add xf86-video-ati + no DRM option to auto-gpu-setup
Thu, 30 Apr 2020
[ 19:33 jwb ] Original commit 
automount 1.7.2 sysutils files touched by this commit FreeBSD's devd(8) based automount solution
sysutils/automount: Upgrade to 1.7.2

Fixes mount permissions issues in previous version
Fixes hang during pkg install
Removed pkg-install script which violated policy against starting services and
replaced with a pkg-message instructing user to restart devd

PR:             ports/246026
Submitted by:   vermaden@interia.pl
Fri, 24 Apr 2020
[ 19:22 jwb ] Original commit 
praat 6.1.13 audio files touched by this commit Phonetics by Computer
audio/praat: Upgrade to 6.1.13

Clean up patches
Switch from OSS to ALSA (upstream default)
Left in and documented patches to ease switch to OSS or JACK in case of
runtime issues
Releasing maintainership as I no longer work with any praat users

Reported by:    portscout
Mon, 20 Apr 2020
[ 12:21 jwb ] Original commit 
afni 20.1.01 science files touched by this commit Advanced Functional Neuro Imaging
science/afni: Upgrade to 20.1.02

Added some common R-cran run dependencies
Removed obsolete reinplace patches
Improved do-install to better fit filesystem hierarchy
Releasing maintainership as I no longer work with any AFNI users

Reported by:    portscout
Wed, 15 Apr 2020
[ 15:22 jwb ] Original commit 
gcta 1.26.0 biology files touched by this commit Genome-wide Complex Trait Analysis
biology/gcta: Genome-wide Complex Trait Analysis

GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate
the proportion of phenotypic variance explained by genome- or chromosome-wide
SNPs for complex traits (the GREML method), and has subsequently extended for
many other analyses to better understand the genetic architecture of complex
traits.
[ 12:50 jwb ] Original commit 
slurm-wlm 20.02.1_1 sysutils files touched by this commit Simple Linux Utility for Resource Management
sysutils/slurm-wlm: Revert error file to stderr when redirect no longer needed

Fixes an oversight in a new patch for 20.02.1
Tue, 14 Apr 2020
[ 12:13 jwb ] Original commit 
py-macs2 2.2.7.1 biology files touched by this commit Identify transcription factor binding sites
biology/py-macs2: Upgrade to 2.2.7.1

Bug fix release

Reported by:    portscout
Sun, 12 Apr 2020
[ 14:31 jwb ] Original commit 
dlpoly-classic 1.8_19 science files touched by this commit Molecular dynamics simulation package
science/dlpoly-classic: Change dependency to openmpi3

This is only a quick unbreak revision.  The port badly needs an upgrade to the
latest version on Gitlab.

PR:             ports/245564
Reported by:    danilo
[ 00:57 jwb ] Original commit 
slurm-wlm 20.02.1 sysutils files touched by this commit Simple Linux Utility for Resource Management
sysutils/slurm-wlm: Upgrade to 20.02.1

Numerous bug fixes and enhancements

Reported by:    portscout
Thu, 9 Apr 2020
[ 16:17 jwb ] Original commit 
fastp 0.20.1 biology files touched by this commit Ultra-fast all-in-one FASTQ preprocessor
biology/fastp: Upgrade to 0.20.1

Fix the plotly.js CDN issue

Reported by:    portscout
[ 12:43 jwb ] Original commit 
star 2.7.3.a biology files touched by this commit Spliced Transcripts Alignment to a Reference
biology/star: Upgrade to 2.7.3a

Several compatibility and feature enhancements
Thu, 2 Apr 2020
[ 13:41 jwb ] Original commit 
kallisto 0.46.2_1 biology files touched by this commit Quantify abundances of transcripts from RNA-Seq data
MFH: r530250

kallisto: Patch for build with GCC

Fixes broken build on GCC-based platforms

PR:             ports/245240
Submitted by:   pkubaj

Approved by:	portmgr (fix build blanket)
Wed, 1 Apr 2020
[ 23:35 jwb ] Original commit 
kallisto 0.46.2_1 biology files touched by this commit Quantify abundances of transcripts from RNA-Seq data
kallisto: Patch for build with GCC

PR:             ports/245240
Submitted by:   pkubaj
Mon, 30 Mar 2020
[ 00:29 jwb ] Original commit 
auto-admin 0.6.1 sysutils files touched by this commit Portable tools for automating systems management
auto-admin: Upgrade to 0.6.1

A few minor bug fixes and enhancements
Sat, 28 Mar 2020
[ 17:37 jwb ] Original commit 
auto-admin 0.6.0 sysutils files touched by this commit Portable tools for automating systems management
auto-admin: Upgrade to 0.6.0

New scripts for octet/hex conversions, iDRAC config and timezone detection
Add ZFS support to auto-pxe-installer-setup
More flexible network settings in auto-pxe-node-discover
Fix egregious bugs in NFS setup scripts
More robust auto-gpu-setup
Improved UI for auto-pkgsrc-setup
More robust auto-update-system
Fri, 20 Mar 2020
[ 18:14 jwb ] Original commit 
canu 2.0 biology files touched by this commit Single molecule sequence assembler
biology/canu: Upgrade to 2.0

Several routine enhancements and bug fixes

Reported by:    portscout
Sun, 15 Mar 2020
[ 23:19 jwb ] Original commit 
slurm-wlm 19.05.5_2 sysutils files touched by this commit Simple Linux Utility for Resource Management
sysutils/slurm-wlm: Remove obsolete and broken REINPLACE

SLURM since 18.08 defaults to /usr/bin/mail if /bin/mail doesn't exist so
this patch is no longer needed and was not functioning correctly anyway

Reported by:    swills
[ 01:34 jwb ] Original commit 
slurm-wlm 19.05.5_1 sysutils files touched by this commit Simple Linux Utility for Resource Management
sysutils/slurm-wlm: Patch build system for clang/lld 10

PR:             ports/244508
Submitted by:   dim
Sat, 7 Mar 2020
[ 19:25 jwb ] Original commit 
jellyfish 2.2.10_8 biology files touched by this commit Fast, memory-efficient counting of k-mers in DNA
biology/jellyfish: Patch for clang 10

Add cast to silence implicit conversion error

PR:             ports/244645
Submitted by:   dim
Sun, 1 Mar 2020
[ 16:01 jwb ] Original commit 
bowtie2 2.4.1 biology files touched by this commit Ultrafast, memory-efficient short read aligner
biology/bowtie2: Upgrade to 2.4.1

Numerous bugfixes and enhancements
Enable experimental support for aarch64

Reported by:    portscout
Wed, 19 Feb 2020
[ 22:34 jwb ] Original commit 
vsearch 2.14.2 biology files touched by this commit Versatile open-source tool for metagenomics
biology/vsearch: Upgrade to 2.14.2

Numerous small bug fixes and enhancements

Reported by:    portscout
Sat, 15 Feb 2020
[ 23:09 jwb ] Original commit 
kallisto 0.46.2 biology files touched by this commit Quantify abundances of transcripts from RNA-Seq data
biology/kallisto: Upgrade to 0.46.2

Kallisto no longer builds in hdf5 by default, but it is still required
for some downstream tools like Sleuth.  Forcing it ON for now, but will
disable it in a future upgrade.

Reported by:    portscout
Sun, 9 Feb 2020
[ 14:23 jwb ] Original commit 
py-macs2 2.2.6_1 biology files touched by this commit Identify transcription factor binding sites
biology/py-macs2: Bump revision for previous run dep addition
[ 14:21 jwb ] Original commit 
py-macs2 2.2.6 biology files touched by this commit Identify transcription factor binding sites
biology/py-macs2: Add missing numpy run depend
Thu, 23 Jan 2020
[ 01:52 jwb ] Original commit 
slurm-wlm 19.05.5 sysutils files touched by this commit Simple Linux Utility for Resource Management
sysutils/slurm-wlm: Upgrade to 19.05.5

Fix recent CVEs
Clean up config file example patches

Reported by:    pkgsrc-security
[ 01:32 jwb ] Original commit 
desktop-installer 0.6.11 sysutils files touched by this commit Quickly configure a FreeBSD desktop system
sysutils/desktop-installer: Upgrade to 0.6.11

Fix a couple regressions
XFCE setup: Remove some obsolete code and enable automount
[ 01:27 jwb ] Original commit 
auto-admin 0.5.1 sysutils files touched by this commit Portable tools for automating systems management
sysutils/auto-admin: Upgrade to 0.5.1

A few minor enhancements for desktop-installer
Thu, 16 Jan 2020
[ 14:55 jwb ] Original commit 
desktop-installer 0.6.10 sysutils files touched by this commit Quickly configure a FreeBSD desktop system
sysutils/desktop-installer: Upgrade to 0.6.10

Eliminate hald config for most desktops
Add mostly-functional external media automount config for lightweight desktops
Move KDE to bsdisks
Add LXQT support
Several minor bug fixes and enhancements, remove some obsolete code
[ 14:05 jwb ] Original commit 
auto-admin 0.5.0 sysutils files touched by this commit Portable tools for automating systems management
sysutils/autoadmin: Upgrade to 0.5.0

Numerous new scripts supporting external media, NFS, pkgsrc, etc
All scripts now install on all platforms for consistent plist
Several bug fixes and dead code removal
Tue, 14 Jan 2020
[ 22:35 jwb ] Original commit 
gemma 0.98.1_3 biology files touched by this commit Genome-wide Efficient Mixed Model Association
biology/gemma: Unbreak build

Conflict between cblas.h and gsl_cblas.h
Sat, 11 Jan 2020
[ 14:20 jwb ] Original commit 
py-macs2 2.2.6 biology files touched by this commit Identify transcription factor binding sites
biology/py-macs2: Upgrade to 2.2.6

Bug fixes and performance improvements
Now require python 3.6+

Reported by:    portscout
Thu, 26 Dec 2019
[ 16:21 jwb ] Original commit 
ncbi-blast+ 2.10.0 biology files touched by this commit NCBI implementation of Basic Local Alignment Search Tool
biology/ncbi-blast+: Upgrade to 2.10.0

Numerous minor bug fixes, enhancements and dependency upgrades
Minor port clean-up
1 patch from previous version upstreamed

Reported by:    portscout
Thu, 19 Dec 2019
[ 01:04 jwb ] Original commit 
bedtools 2.29.2 biology files touched by this commit Toolset for genome set arithmetic such as intersect, union
biology/bedtools: Upgrade to 2.29.2

Fixed a bug that mistakenly removed a BAM/CRAM header line

Reported by:    portscout
Wed, 11 Dec 2019
[ 15:13 jwb ] Original commit 
bedtools 2.29.1 biology files touched by this commit Toolset for genome set arithmetic such as intersect, union
biology/bedtools: Upgrade to 2.29.1

Several important bug fixes.

Reported by:    portscout
Thu, 28 Nov 2019
[ 05:46 jwb ] Original commit 
unanimity 3.4.1_3 biology  Deleted Broken Deprecated Expired Ignore files touched by this commit Pacific Biosciences consensus library and applications
biology/unanimity: Remove erroneous BROKEN

Unsure why this was marked unfetchable.  Fetch works fine and the port is
still useful, though it cannot be upgraded to newer releases, which are
closed-source.
Wed, 27 Nov 2019
[ 18:18 jwb ] Original commit 
desktop-installer 0.6.9 sysutils files touched by this commit Quickly configure a FreeBSD desktop system
sysutils/desktop-installer: Upgrade to 0.6.9

Prevent non-zero exit on autofs setup from terminating desktop-installer
Tue, 26 Nov 2019
[ 16:25 jwb ] Original commit 
py-multiqc 1.8 biology files touched by this commit Aggregate bioinformatics analysis reports across samples and tools
biology/py-multiqc: Upgrade to 1.8

Major enhancements including 6 new modules and improvements to existing modules
Numerous minor fixes and enhancements

Reported by:    portscout
[ 16:20 jwb ] Original commit 
p5-TrimGalore 0.6.5 biology files touched by this commit Wrapper around Cutadapt and FastQC for adapter and quality trimming
biology/p5-TrimGalore: Upgrade to 0.6.5

Minor bugfixes and enhancements

Reported by:    portscout
Sun, 24 Nov 2019
[ 15:53 jwb ] Original commit 
pbbam 0.18.0_3 biology files touched by this commit PacBio BAM C++ library, with SWIG bindings
pbcopper 0.4.1_3 biology  Broken Ignore files touched by this commit Core C++ library for Pacific Biosciences tools
pbseqan g20171011 biology  Deprecated files touched by this commit Pacific Biosciences patched and stripped down SeqAn
unanimity 3.4.1_3 biology  Deleted Broken Deprecated Expired Ignore files touched by this commit Pacific Biosciences consensus library and applications
biology/unanimity and dependencies: Flag as no longer open source

PacBio now provides unanimity only as a binary package through bioconda.
See https://github.com/PacificBiosciences/ccs.
Sat, 23 Nov 2019
[ 18:10 jwb ] Original commit 
desktop-installer 0.6.8 sysutils files touched by this commit Quickly configure a FreeBSD desktop system
sysutils/desktop-installer: Upgrade to 0.6.8

Partially automate GPU/DRM setup with auto-gpu-setup
Fix KDE5 test startup
Begin streamlining UI to broaden target audience
[ 18:04 jwb ] Original commit 
auto-admin 0.4.9 sysutils files touched by this commit Portable tools for automating systems management
sysutils/auto-admin: Upgrade to 0.4.9

Add auto-remove-from-group
Rename auto-detect-gpu to auto-gpu-setup to reflect new functionality
Improvements to auto-pkgsrc-setup
Other minor fixes and enhancements
[ 14:45 jwb ] Original commit 
py-cutadapt 2.7 biology files touched by this commit Trim adapters from high-throughput sequencing reads
biology/py-cutadapt: Upgrade to 2.7

Numerous minor fixes and enhancements.
Upstreamed setup.py patches for dependency versions.

Reported by:    portscout
[ 14:41 jwb ] Original commit 
py-xopen 0.8.4 archivers files touched by this commit Open compressed files transparently
archivers/py-xopen: Upgrade to 0.8.4

Needed for py-cutadapt 2.7
[ 14:40 jwb ] Original commit 
py-dnaio 0.4.1 biology files touched by this commit Read and write FASTQ and FASTA
biology/py-dnaio: Upgrade to 0.4.1

Needed for py-cutadapt 2.7
Sun, 17 Nov 2019
[ 15:00 jwb ] Original commit 
haplohseq 0.1.2_1 biology  Deprecated Expiration Date files touched by this commit Identify regions of allelic imbalance
biology/haplohseq: Switch to distfile with example data

Add script to run on example input
Minor fix to report inadequate VCF input
Sat, 16 Nov 2019
[ 21:56 jwb ] Original commit 
R-cran-optparse 1.6.4 devel files touched by this commit Command line flag parser inspired by Python's optparse
devel/R-cran-optparse: Command line flag parser inspired by Python's optparse

Command line parser inspired by Python's 'optparse' library to be used with
Rscript to write "#!" shebang scripts that accept short and long flag/options.
[ 16:50 jwb ] Original commit 
R-cran-getopt 1.20.3 devel files touched by this commit Accept short and long flags in Rscript
devel/R-cran-getopt: Accept short and long flags in Rscript

Package designed to be used with Rscript to write "#!" shebang scripts that
accept short and long flags/options. Many users will prefer using instead the
packages optparse or argparse which add extra features like automatically
generated help option and usage, support for default values, positional
argument support, etc.
Fri, 8 Nov 2019
[ 14:03 jwb ] Original commit 
canu 1.9 biology files touched by this commit Single molecule sequence assembler
biology/canu: Upgrade to 1.9

Numerous bug fixes and enhancements

Reported by:    portscout
Wed, 6 Nov 2019
[ 00:18 jwb ] Original commit 
kallisto 0.46.1 biology files touched by this commit Quantify abundances of transcripts from RNA-Seq data
biology/kallisto: Upgrade to 0.46.1

Minor bug fixes and enhancements

Reported by:    portscout
Sun, 6 Oct 2019
[ 22:18 jwb ] Original commit 
star 2.7.2.d biology files touched by this commit Spliced Transcripts Alignment to a Reference
biology/star: Upgrade to 2.7.2d

Fix chimeric output bug.

Numerous other minor fixes and enhancements since 2.7.0.

Reported by:    portscout
[ 21:34 jwb ] Original commit 
fastahack 1.0.0 biology files touched by this commit Utility for indexing and sequence extraction from FASTA files
biology/fastahack: Upgrade to 1.0.0

Very few changes, upstream just finally got around to cutting a release.

Reported by:    portscout
Fri, 27 Sep 2019
[ 00:49 jwb ] Original commit 
tophat 2.1.1 biology  Deprecated Expiration Date files touched by this commit Fast splice junction mapper for RNA-Seq reads
biology/tophat: Fast splice junction mapper for RNA-Seq reads

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq
reads to mammalian-sized genomes using the ultra high-throughput short read
aligner Bowtie, and then analyzes the mapping results to identify splice
junctions between exons.

Note:

TopHat has been Superseded by HISAT2 and is no longer maintained upstream.
This port is provided mainly for revisiting old studies where TopHat was used.
Mon, 23 Sep 2019
[ 16:09 jwb ] Original commit 
py-multiqc 1.7 biology files touched by this commit Aggregate bioinformatics analysis reports across samples and tools
biology/py-multiqc: Aggregate bioinformatics analysis reports

MultiQC searches a given directory for analysis logs and compiles an HTML
report. It's a general use tool, perfect for summarising the output from
numerous bioinformatics tools.
Sun, 22 Sep 2019
[ 19:06 jwb ] Original commit 
packmol 18.169 science files touched by this commit Pack molecules in defined regions of space
science/packmol: Pack molecules in defined regions of space

PACKMOL creates an initial point for molecular dynamics simulations by packing
molecules in defined regions of space. The packing guarantees that short range
repulsive interactions do not disrupt the simulations.
[ 16:15 jwb ] Original commit 
py-lzstring 1.0.4 archivers files touched by this commit LZ-based in-memory string compression
archivers/py-lzstring: LZ-based in-memory string compression

LZ-based, in-memory string compression module, based on the LZ-String
javascript module.
[ 15:54 jwb ] Original commit 
py-spectra 0.0.11 graphics files touched by this commit Color scales and color conversion made easy for Python
graphics/py-spectra: Color scales and color conversion made easy for Python

Spectra is a Python library that makes color math, color scales, and
color-space conversion easy.

Support for:

    Color scales
    Color ranges
    Color blending
    Brightening/darkening colors
    Saturating/desaturating colors
    Conversion to/from multiple color spaces

Spectra is built on colormath and grapefruit. Spectra is enormously inspired by
chroma.js and d3's scales.
Sat, 21 Sep 2019
[ 02:51 jwb ] Original commit 
p5-TrimGalore 0.6.4 biology files touched by this commit Wrapper around Cutadapt and FastQC for adapter and quality trimming
biology/p5-TrimGalore: Upgrade to 0.6.4

Improved adapter autodetection, minor bug fixes.
[ 02:44 jwb ] Original commit 
fastqc 0.11.8 biology files touched by this commit Quality control tool for high throughput sequence data
biology/fastqc: Upgrade to 0.11.8

Minor bug fixes and edge case handling.

Minor Makefile clean up.
Mon, 16 Sep 2019
[ 01:07 jwb ] Original commit 
haplohseq 0.1.2 biology  Deprecated Expiration Date files touched by this commit Identify regions of allelic imbalance
biology/haplohseq: Identify regions of allelic imbalance

Haplohseq identifies regions of allelic imbalance (AI) in sequencing data
obtained from impure samples where AI events exist in a potentially low
proportion of cells in the sample.  Input to the software includes a VCF file
of genotypes and estimated phased genotypes.
Sat, 14 Sep 2019
[ 16:02 jwb ] Original commit 
slurm-wlm 19.05.1.2_2 sysutils files touched by this commit Simple Linux Utility for Resource Management
sysutils/slurm-wlm: Temporary patch to silence job accounting errors

Disables linux-specific code when using jobacct_gather/linux for now.
Long-term solution is to revamp job accounting code for FreeBSD.
[ 14:45 jwb ] Original commit 
trimmomatic 0.39 biology files touched by this commit Flexible read trimming tool for Illumina NGS data
biology/trimmomatic: Upgrade to 0.39

Add convenience script to run without knowing the location of the Java jar
[ 12:25 jwb ] Original commit 
py-xopen 0.8.2 archivers files touched by this commit Open compressed files transparently
py-xopen: Upgrade to 0.8.2

Add pigz dep for parallel gzip
Fri, 13 Sep 2019
[ 13:21 jwb ] Original commit 
bedtools 2.29.0 biology files touched by this commit Toolset for genome set arithmetic such as intersect, union
biology/bedtools: Upgrade to 2.29.0

Add test target to run test scripts in dist

Reported by:    portscout
[ 13:17 jwb ] Original commit 
py-cutadapt 2.5 biology files touched by this commit Trim adapters from high-throughput sequencing reads
biology/py-cutadapt: Upgrade to 2.5

Add pigz run depend for parallel gzip/gunzip
Sat, 17 Aug 2019
[ 15:11 jwb ] Original commit 
desktop-installer 0.6.7 sysutils files touched by this commit Quickly configure a FreeBSD desktop system
sysutils/desktop-installer: Upgrade to 0.6.7

Disable bsdstats install (bsdstats.org is offline)
Numerous improvements to user interface
Tue, 13 Aug 2019
[ 15:30 jwb ] Original commit 
bolt-lmm 2.3.4 biology files touched by this commit Mixed model association testing and variance component analysis
biology/bolt-lmm: Upgrade to 2.3.4

Remove previously upstreamed patches
New Makefile patch that preserves default behavior and should be palatable
to upstream
Sun, 4 Aug 2019
[ 23:48 jwb ] Original commit 
bolt-lmm 2.3.2_2 biology files touched by this commit Mixed model association testing and variance component analysis
PR:             239613
Submitted by:   pkubaj
Thu, 25 Jul 2019
[ 21:54 jwb ] Original commit 
desktop-installer 0.6.6 sysutils files touched by this commit Quickly configure a FreeBSD desktop system
sysutils/desktop-installer: Upgrade to 0.6.6

Remove obsolete qt/kde 4 references
Default to no flashplayer on all platforms
Factor out flashplayer setup to sysutils/auto-admin
Disable webcamd setup for now (interferes with uhid)
Other clean up and minor enhancements
[ 21:46 jwb ] Original commit 
auto-admin 0.4.8 sysutils files touched by this commit Portable tools for automating systems management
sysutils/auto-admin: Upgrade to 0.4.8

FreeBSD changes:

Roll auto-add-linproc-mount into auto-install-linux_base
Remove obsolete auto-amd-nfs-setup, auto-kdm3-toggle
Add scripts for installing and updating infininband kernel
Factor auto-install-linux-flash out of desktop-installer

New common scripts:

auto-idrac-passwd
auto-fetch-install-media
auto-install-media-distname
auto-lock-local-pw, auto-unlock-local-pw
auto-root-check
auto-useradd
auto-user-admin
Sun, 21 Jul 2019
[ 00:10 jwb ] Original commit 
slurm-wlm 19.05.1.2 sysutils files touched by this commit Simple Linux Utility for Resource Management
sysutils/slurm-wlm: Upgrade to 19.05.1-2

Resolves CVE-2019-12838
Add NOT_FOR_ARCHS since upstream has deprecated 32-bit architectures
Fri, 12 Jul 2019
[ 23:58 jwb ] Original commit 
ncbi-blast+ 2.9.0_2 biology files touched by this commit NCBI implementation of Basic Local Alignment Search Tool
ncbi-blast+: Unbreak build with gcc8 following gcc9 patch

GCC 8 and 9 are incompatible in handling const variables with OpenMP
default(none).  All const variables default to shared even with default(none)
present.  8 errors out if a const variable is explicitly defined as shared and
9 requires an explicit definition.

Using an upstream trunk patch for now, which checks the compiler version.
Also discussing more portable approaches to avoid future issues.

Reported by:    jrm
Thu, 11 Jul 2019
[ 13:53 jwb ] Original commit 
ncbi-blast+ 2.9.0_1 biology files touched by this commit NCBI implementation of Basic Local Alignment Search Tool
ncbi-blast+: Fix build with gcc9

GCC 9 requires OpenMP variables to be explicitly defined as shared or private
where earlier versions fell back on default.  New patch sent upstream.

PR:             238471
Reported by:    gerald
Tue, 18 Jun 2019
[ 19:00 jwb ] Original commit 
afni 19.1.20 science files touched by this commit Advanced Functional Neuro Imaging
science/afni: Upgrade to 19.1.20

Upstreamed FreeBSD patches, other minor fixes and enhancements

Reported by:    portscout, Rick Reynolds (NIH)
Fri, 14 Jun 2019
[ 00:37 jwb ] Original commit 
ncbi-blast+ 2.9.0 biology files touched by this commit NCBI implementation of Basic Local Alignment Search Tool
biology/ncbi-blast+: Fix build on powerpc64, add run dep for update_blastdb.pl
[ 00:21 jwb ] Original commit 
slurm-wlm 18.08.7 sysutils files touched by this commit Simple Linux Utility for Resource Management
sysutils/slurm-wlm: Revert previous change enabling Linux option by default

Option is not actually necessary anymore to enable linproc parsing code.
It merely adds a linux_base dependency now.
Thu, 13 Jun 2019
[ 23:53 jwb ] Original commit 
slurm-wlm 18.08.7 sysutils files touched by this commit Simple Linux Utility for Resource Management
sysutils/slurm-wlm: Enable jobacct_gather/linux by default

Currently required to terminate jobs exceeding their memory allocation
(until jobacct_gather/freebsd is implemented)
Wed, 12 Jun 2019
[ 23:53 jwb ] Original commit 
ncbi-blast+ 2.9.0 biology files touched by this commit NCBI implementation of Basic Local Alignment Search Tool
biology/ncbi-blast+: Upgrade to 2.9.0

Fixes build issue with gcc9

PR:             238471
Reported by:    gerald
[ 15:24 jwb ] Original commit 
kallisto 0.46.0 biology files touched by this commit Quantify abundances of transcripts from RNA-Seq data
biology/kallisto: Upgrade to 0.46.0

Reported by:    portscout
Sat, 8 Jun 2019
[ 19:14 jwb ] Original commit 
afni 19.1.18 science files touched by this commit Advanced Functional Neuro Imaging
science/afni: Upgrade to 19.1.18

Minor bugfixes/enhancements
Sat, 1 Jun 2019
[ 12:59 jwb ] Original commit 
afni 19.1.14 science files touched by this commit Advanced Functional Neuro Imaging
science/afni: Upgrade to 19.1.14

Minor bug fixes and enhancements, some FreeBSD patches upstreamed
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