00:58 Wen Heping (wen) 

biology/py-newick: Add new port

A python module to read and write the Newick format.

    d9d5b36

21:23 Rene Ladan (rene) 

biology/recombine: Remove expired port

2024-01-17 biology/recombine: Upstream advises to use biology/lamarc

    2f8680e

18:29 Muhammad Moinur Rahman (bofh) 

biology/seqio: Remove expired port

2024-01-17 biology/seqio: Upstream last release was in 2000

    b4b8e40

18:29 Muhammad Moinur Rahman (bofh) 

biology/sim4: Remove expired port

2024-01-17 biology/sim4: Upstream last update was in 2005

    b8f4ba2

15:19 Jason W. Bacon (jwb) 

biology/py-macs3: Peak caller for TF binding sites

MACS (Model-based Analysis of ChIP-Seq) is a tool for identifying
transcription factor (TF) binding sites.   Such sites are generated
by CHiP-Seq (CHromatin immuno-Precipitation sequencing) and ATAC-Seq
(Assay for Transposase Accessible Chromatin Sequencing).  MACS
identifies "peaks" in the genome sequence, which are areas enriched
in bound TFs or accessible chromatin.

    fabf2f6

12:55 Muhammad Moinur Rahman (bofh) 

biology/R-cran-BiocGenerics: New port

The package defines many S4 generic functions used in Bioconductor.

WWW: https://bioconductor.org/packages/release/bioc/html/BiocGenerics.html

    4cdc852

12:55 Muhammad Moinur Rahman (bofh) 

biology/R-cran-Biobase: New port

Functions that are needed by many other packages or which replace R
functions.

WWW: https://bioconductor.org/packages/Biobase

    82e85eb

12:55 Muhammad Moinur Rahman (bofh) 

biology/R-cran-BiocManager: New port

The BiocManager package, as the modern successor package to
BiocInstaller, allows users to install and manage packages from the
Bioconductor project. Bioconductor focuses on the statistical analysis
and comprehension of high-throughput genomic data.

WWW: https://bioconductor.github.io/BiocManager/

    5051eb6

15:41 Jason W. Bacon (jwb) 

biology/py-htseq: Python library for sequence analysis

HTSeq is a Python library to facilitate programmatic analysis of data
from high-throughput sequencing (HTS) experiments. A popular component
of HTSeq is htseq-count, a script to quantify gene expression in bulk
and single-cell RNA-Seq and similar experiments.

    505bb0d

23:06 Jason W. Bacon (jwb) 

biology/salmon: Transcript-level quantification of RNA-seq

Salmon is a wicked-fast program to produce a highly-accurate,
transcript-level quantification estimates from RNA-seq data. Salmon
achieves is accuracy and speed via a number of different innovations,
including the use of quasi-mapping (accurate but fast-to-compute
proxies for traditional read alignments), and massively-parallel
stochastic collapsed variational inference. The result is a versatile
tool that fits nicely into many differnt pipelines.

    64a6421

22:24 Yuri Victorovich (yuri) 

biology/btllib: New port: Bioinformatics Technology Lab common code library

    29bea60

21:38 Yuri Victorovich (yuri) 

biology/seqwish: New port: Assembly By Short Sequences: parallel, paired-end
sequence assembler

    04d04b8

21:54 Yuri Victorovich (yuri) 

biology/locarna: New port: LocARNA provides several tools for the structural
analysis of RNA

    5560f5f

01:44 Yuri Victorovich (yuri) 

biology/mashmap: New port: Fast approximate aligner for long DNA sequences

    2512450

13:38 Jason W. Bacon (jwb) 

biology/bifrost: Parallel tool for de Bruijn graphs

Bifrost is a tool and API for parallel construction, indexing and
querying of colored and compacted de Bruijn graphs from FASTA/FASTQ
DNA/RNA sequence files.

    9644117

21:23 Jason W. Bacon (jwb) 

biology/chip-seq: Metaport for ChIP-Seq analysis

Metaport to install tools for typical ChIP-Seq analysis, including QC,
adapter trimming, alignment, and differential analysis.

Presently identical to biology/atac-seq, but may diverge in the future.

    fddb1ea

14:27 Jason W. Bacon (jwb) 

biology/bcf-score: Bcftools plugins for GWAS-VCF summary statistics

Score is a set of tools in the form of a bcftools plugin, for handling
and converting summary statistics files following the GWAS-VCF
specification.

    68c12d4

19:09 Jason W. Bacon (jwb) 

biology/wfa2-lib: Exact gap-affine algorithm using homology

The wavefront alignment (WFA) algorithm is an exact gap-affine
algorithm that takes advantage of homologous regions between the
sequences to accelerate the alignment process.  Unlike traditional
dynamic programming algorithms that run in quadratic time, the WFA runs
in time O(ns+s^2), proportional to the sequence length n and the
alignment score s, using O(s^2) memory (or O(s) using the
ultralow/BiWFA mode). Moreover, the WFA algorithm exhibits simple
computational patterns that the modern compilers can automatically
vectorize for different architectures without adapting the code.

    595d0da

23:47 Jason W. Bacon (jwb) 

biology/atac-seq: Metaport for ATAC-Seq analysis

Metaport to install tools for typical ATAC-Seq analysis, including QC,
adapter trimming, alignment, and differential analysis.

    d2c13cc

08:32 Yuri Victorovich (yuri) 

biology/py-biosig: New port: Library for reading and writing different biosignal
data format

    8ce2f72

17:30 Jason W. Bacon (jwb) 

biology/rna-seq: Metaport for RNA-Seq analysis

Metaport to install tools for typical RNA-Seq analysis, including QC,
adapter trimming, alignment, and differential analysis.

    8e926be

17:17 Jason W. Bacon (jwb) 

biology/fasda: Fast and simple differential analysis

FASDA aims to provide a fast and simple differential analysis tool
that just works and does not require any knowledge beyond basic Unix
command-line skills. The code is written entirely in C to maximize
efficiency and portability, and to provide a simple command-line user
interface.

    455ea91

15:41 Yuri Victorovich (yuri) 

biology/py-pyrodigal: New port: Python binding for Prodigal, an ORF finder for
genomes and metagenomes

    29c79a3

11:04 Yuri Victorovich (yuri) 

biology/metaeuk: New port: Gene discovery and annotation for large-scale
eukaryotic metagenomics

    affc650

23:55 Yuri Victorovich (yuri) 

biology/augustus: New port: Genome annotation tool

    8b43ef5

03:08 Yuri Victorovich (yuri) 

biology/barrnap: New port: BAsic Rapid Ribosomal RNA Predictor

    a7eec55

16:39 Jason W. Bacon (jwb) 

biology/megahit: Ultra-fast single-node metagenomics assembly

MEGAHIT is a single node assembler for large and complex metagenomics
NGS reads, such as soil. It makes use of succinct de Bruijn graph
(SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize
a CUDA-enabled GPU to accelerate its SdBG contstruction.

    acb3a0d

07:05 Yuri Victorovich (yuri) 

biology/libcombine: New port: C++ library for working with the COMBINE archive
format

    47f90fe

04:06 Yuri Victorovich (yuri) 

biology/py-valerius: New port: Python bioinformatics tools

    f830071

20:30 Yuri Victorovich (yuri) 

biology/kmcp: New port:  Accurate metagenomic profiling & fast large-scale
genome searching

    d17e673

01:33 Yuri Victorovich (yuri) 

biology/ngs-sdk: Revert: Un-remove, ngs was moved into sra-tools

This reverts commit 1cb8897f610a381ddf2802eb09acfba97b15b505.

sra-tools needs to be updated first.

Reported by:	Tomoaki AOKI <junchoon@dec.sakura.ne.jp>, perciva@

    d3e9586

19:03 Yuri Victorovich (yuri) 

biology/ngs-sdk: Remove, ngs was moved into sra-tools

    1cb8897

07:52 Yuri Victorovich (yuri) 

biology/mopac: Move to science/mopac; Add TIMESTAMP to distinfo; Take
maintainership

    db283c3

17:37 Yuri Victorovich (yuri) 

biology/py-mrcfile: New port: MRC file I/O library which is used in structural
biology

    8db0b60

12:25 Jason W. Bacon (jwb) 

biology/fastq-trim: Lightening fast sequence read trimmer

Fastq-trim is a lightening fast read trimming tool for QA of
DNA and RNA reads prior to analyses such as RNA-Seq.

    a47115b

19:38 Jason W. Bacon (jwb) 

biology/py-bcbio-gff: Read and write Generic Feature Format (GFF)

Read and write Generic Feature Format (GFF) with Biopython integration.

Also adding py-dna-features-viewer to Makefile, missed on last commit

    d936c94

20:50 Jason W. Bacon (jwb) 

biology/libgff: GFF/GTF parsing library based on GCLib

This is an attempt to perform a simple "libraryfication" of the GFF/GTF
parsing code that is used in GFFRead codebase. There are not many
(any?) relatively lightweight GTF/GFF parsers exposing a C++ interface,
and the goal of this library is to provide this functionality without
the necessity of drawing in a heavy-weight dependency like SeqAn. Note:
This library draws directly from the code in GFFRead and GCLib, and
exists primarily to remove functionality (and hence code) that is
unnecessary for our downstream purposes. In the future, it may be
appropriate to just replace this library wholesale with GCLib.

    864d4fd

13:41 Jason W. Bacon (jwb) 

biology/bio-mocha: bcftools plugin for mosaic chromosomal alterations

MoChA is a bcftools plugin released under the MIT license for mosaic
chromosomal alteration detection and analysis from DNA microarray or
whole genome sequence data. It can be used both with Illumina and
Affymetrix data. It can also be used for detection of germline copy
number variants. Data can be prepared in usable file formats using the
gtc2vcf plugin.

    9152cfc

20:49 Jason W. Bacon (jwb) 

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

GFF/GTF utility providing format conversions, filtering, FASTA sequence
extraction and more.

    8d2198b

15:57 Po-Chuan Hsieh (sunpoet) 

*/Makefile: Sort SUBDIRs

    70b8183

11:51 Jason W. Bacon (jwb) 

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

deepTools contains useful modules to process the mapped reads data for
multiple quality checks, creating normalized coverage files in standard
bedGraph and bigWig file formats, that allow comparison between
different files (for example, treatment and control). Finally, using
such normalized and standardized files, deepTools can create many
publication-ready visualizations to identify enrichments and for
functional annotations of the genome.

    799d4cc

21:21 Jason W. Bacon (jwb) 

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

Fully match upstream name

    ad5a060

18:57 Antoine Brodin (antoine) 

biology/py-pybigwig: remove, duplicate of biology/py-bigwig

    6a22629

16:02 Jason W. Bacon (jwb) 

biology/py-pybigwig: Fix poudriere build

Typo in post-install

    c69e97e

13:03 Jason W. Bacon (jwb) 

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

py-bigwig is a python extension, written in C, for quick access to
bigBed files and access to and creation of bigWig files. This extension
uses libBigWig for local and remote file access.

    904a889

12:53 Jason W. Bacon (jwb) 

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

py2bit is a python extension, written in C, for quick access to 2bit
files for randomly accessible, packed nucleotide sequences. The
extension uses lib2bit for file access.

    d923440

16:40 Jason W. Bacon (jwb) 

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

Utilities for working on SAM/BAM files from The Center for Statistical
Genetics at the University of Michigan School of Public Health.  It
includes numerous functions such as splitting, merging, trimming reads,
filtering, validation, diff, etc.

    cdf2ff2

17:20 Yuri Victorovich (yuri) 

biology/libneurosim: New port: Common interfaces for neuronal simulators

    c38052d

03:35 Po-Chuan Hsieh (sunpoet) 

*/Makefile: Sort SUBDIRs

    6e0aa01

18:15 Yuri Victorovich (yuri) 

biology/py-libsedml: New port: SED-ML library for Python

    d8c851d

18:15 Yuri Victorovich (yuri) 

biology/libsedml: New port: C++ SED-ML library

    dd804e9

06:47 Yuri Victorovich (yuri) 

biology/py-libnuml: New port: Numerical Markup Language for Python

    74c9986

06:47 Yuri Victorovich (yuri) 

biology/libnuml: New port: C++ library for Numerical Markup Language

    ad2bdb6

20:32 Jason W. Bacon (jwb) 

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

sam2pairwise takes a SAM file and uses the CIGAR and MD tag to
reconstruct the pairwise alignment of each read.

    e61df5e

12:55 Jason W. Bacon (jwb) 

biology/py-pywgsim: Modified wgsim genomic data simulator

pywgsim is a modified version of the wgsim short read simulator.  The
code for wgsim has been modified to allow visualizing the simulated
mutations as a GFF file.

    c085af1

13:09 Jason W. Bacon (jwb) 

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

Biolibc-tools is a collection of simple fast, memory-efficient,
programs for processing biological data.  These are simple programs
built on biolibc that are not complex enough to warrant a separate
project.

    904aa60

17:28 Jason W. Bacon (jwb) 

biology/bfc: Correct sequencing errors from Illumina sequencing data

BFC is a standalone high-performance tool for correcting sequencing
errors from Illumina sequencing data. It is specifically designed for
high-coverage whole-genome human data, though also performs well for
small genomes.

    2e559ca

17:26 Jason W. Bacon (jwb) 

biology/flash: Fast Length Adjustment of SHort reads

FLASH (Fast Length Adjustment of SHort reads) is a very fast and
accurate software tool to merge paired-end reads from next-generation
sequencing experiments. FLASH is designed to merge pairs of reads when
the original DNA fragments are shorter than twice the length of reads.
The resulting longer reads can significantly improve genome assemblies.
They can also improve transcriptome assembly when FLASH is used to
merge RNA-seq data.

    615c521

21:30 Yuri Victorovich (yuri) 

biology/py-PySCeS: New port: Python Simulator for Cellular Systems

    1c0e78e

21:30 Yuri Victorovich (yuri) 

biology/py-python-libsbml: New port: LibSBML Python API

    10875d9

07:05 Yuri Victorovich (yuri) 

biology/sigviewer: New port: Viewing application for biosignals

    aa9a35be

02:51 Yuri Victorovich (yuri) 

biology/biosig: New port: Library for reading and writing different biosignal
data format

    df70b7e

13:34 Jason W. Bacon (jwb) 

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

The ont_fast5_api is a simple interface to HDF5 files of the Oxford
Nanopore .fast5 file format. It provides:

    o Implementation of the fast5 file schema using h5py library
    o Methods to interact with and reflect the fast5 file schema
    o Tools to convert between multi_read and single_read formats
    o Tools to compress/decompress raw data in files

    5797d6a

12:26 Jason W. Bacon (jwb) 

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

ErmineJ performs analyses of gene sets in high-throughput genomics data
such as gene expression profiling studies. A typical goal is to
determine whether particular biological pathways are "doing something
interesting" in an experiment that generates long lists of candidates.
The software is designed to be used by biologists with little or no
informatics background (but if you do, you might be interested in the
CLI or the R support).

    e44f917

17:00 Jason W. Bacon (jwb) 

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

Goatools is a python library for processing Gene Ontology (GO) terms.  It
includes routines for processing, filtering, and visualizing GO data.

    7fd4d44

17:31 Jason W. Bacon (jwb) 

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

MMseqs2 (Many-against-Many sequence searching) is a software suite to search
and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source
GPL-licensed software implemented in C++ for FreeBSD, Linux, MacOS, and (via
via cygwin) Windows. The software is designed to run on multiple cores and
servers and exhibits very good scalability. MMseqs2 can run 10000 times
faster than BLAST. At 100 times its speed it achieves almost the same
sensitivity. It can perform profile searches with the same sensitivity as
PSI-BLAST at over 400 times its speed.

    cf14bbb

17:55 Jason W. Bacon (jwb) 

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

SRA tools is a toolkit for using data in the INSDC Sequence Read Archives.

SRAs operated by International Nucleotide Sequence Database Collaboration
houses sequence reads and alignments generated by "next-gen" sequencers.

This port is a bit convoluted due to the fact that the sra-tools build
requires access to the ncbi-vdb source tree.  Hence, ncbi-vdb is treated
as a submodule here rather than a separate library port.  We are working
with upstream with hope for long-term improvements.

    69656bf

21:56 Jason W. Bacon (jwb) 

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

Biostar-Tools is a metaport for installing all the tools necessary to work
through the Biostar Handbook, except for bedGrapToBigWig, which has license
restrictions.  If you need bedGraphToBigWig, run

    cd /usr/ports/biology/ucsc-userapps && make install clean

    6df92a0

16:40 Jason W. Bacon (jwb) 

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

Classify ChIP/ATAC-Seq peaks based on features provided in a GFF

Peaks are provided in a BED file sorted by chromosome and position.
The GFF must be sorted by chromosome and position, with gene-level
features separated by ### tags and each gene organized into
subfeatures such as transcripts and exons.  This is the default for
common data sources.

    5a2a6eb

22:25 Yuri Victorovich (yuri) 

biology/taxonkit: New port: Practical and efficient NCBI taxonomy toolkit

    5b018ca

22:25 Yuri Victorovich (yuri) 

biology/unikmer: New port: Toolkit for nucleic acid k-mer analysis, set
operations on k-mers

    be2fb2f

01:21 Yuri Victorovich (yuri) 

New port: biology/seqan3: C++ header-only library for biological sequence
analysis

    37be696

17:47 Antoine Brodin (antoine) 

Hook biology/ucsc-userapps to the build

    28164db

23:40 Jason W. Bacon (jwb) 

biology/ncbi-entrez-direct: Access to the NCBI's interconnected databases

Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected
databases (publication, sequence, structure, gene, variation, expression, etc.)
from a UNIX terminal window.

    ab50f84

04:22 Yuri Victorovich (yuri) 

New port: biology/py-resdk: Resolwe SDK to interact with Resolwe server and
Resolwe Bioinformatics

    b9f16ea

18:46 Jason W. Bacon (jwb) 

biology/snpeff: Genetic variant annotation and effect prediction toolbox

Genetic variant annotation and functional effect prediction toolbox. It
annotates and predicts the effects of genetic variants on genes and proteins
(such as amino acid changes).

    5164d38

16:21 Jason W. Bacon (jwb) 

biology/bbmap: BBMap short read aligner, and other bioinformatic tools

This package includes BBMap, a short read aligner, as well as various other
bioinformatic tools. It is written in pure Java, can run on any platform, and
has no dependencies other than Java being installed (compiled for Java 6 and
higher). All tools are efficient and multithreaded.

    15458df

13:53 Jason W. Bacon (jwb) 

biology/readseq: Read and reformat biosequences, Java command-line version

Sequence reading library developed by the Ribosomal Database Project.  It can
handle genbank, embl, fasta, fastq, sff and sto files, can read from files or
streams, and can handle indexing files.

    49a1ada

21:04 Yuri Victorovich (yuri) 

New port: biology/seqkit: Cross-platform and ultrafast toolkit for FASTA/Q file
manipulation

    2aa37d8

23:37 Jason W. Bacon (jwb) 

biology/py-crossmap: Lift over genomics coordinates between assemblies

CrossMap is a program for genome coordinates conversion between different
assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used
file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF,
and gVCF.

    9128727

23:24 Jason W. Bacon (jwb) 

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

A python extension, written in C, for quick access to bigBed files and access
to and creation of bigWig files. This extension uses libBigWig for local and
remote file access.

    dfcece2

09:29 Yuri Victorovich (yuri) 

New port: biology/ncbi-vdb: NCBI's virtualized back-end for accessing Sequence
Read Archive

PR:		223273
Submitted by:	Motomichi Matsuzaki <mzaki@niid.go.jp> (original version)

    d55fba4

17:54 Rene Ladan (rene) 

Remove expired ports:

2021-04-01 ftp/wzdftpd: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 astro/roadmap: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 games/cosmo: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 games/bomberinstinct: Unmaintained and dead upstream, does not build
with -fno-common (llvm 11)
2021-04-01 games/drm: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 games/bygfoot: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 games/cre: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 irc/hybserv: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 irc/xaric: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 mail/elmo: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 misc/cave: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 security/bugs: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 security/dmitry: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 security/doorman: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 shells/esh: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 sysutils/cpu: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 textproc/libcrm114: No known users, dead upstream
2021-04-01 x11/wmmatrix: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 x11/wmxss: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 x11/tycoon: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 x11/xgrab: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 x11/xbanner: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 x11/bricons: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 x11/xmon: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 games/cavezofphear: Unmaintained and dead upstream, does not build
with -fno-common (llvm 11)
2021-04-01 astro/saoimage: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 audio/ksmp3play: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 audio/jamin: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 audio/musicbox-tag-editor: Unmaintained and dead upstream, does not
build with -fno-common (llvm 11)
2021-04-01 audio/nspmod: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 audio/cdplay: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 audio/gimmix: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 audio/ghostess: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 audio/wmrecord: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 audio/toolame: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 audio/shout: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 biology/grappa: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 biology/phylip: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 biology/lagan: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 cad/varkon: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 cad/transcalc: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 comms/seyon: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 comms/efax: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 converters/vda2fbd: Unmaintained and dead upstream, does not build
with -fno-common (llvm 11)
2021-04-01 converters/shftool: Unmaintained and dead upstream, does not build
with -fno-common (llvm 11)
2021-04-01 devel/openzz: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 devel/sourcenav: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 devel/gb: Unmaintained and dead upstream
2021-04-01 dns/checkdns: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 dns/inadyn-mt: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 editors/gate: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 editors/thoteditor: Unmaintained and dead upstream, does not build
with -fno-common (llvm 11)
2021-04-01 emulators/cinc: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 emulators/e-uae: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 emulators/dtcyber: Unmaintained and dead upstream, does not build
with -fno-common (llvm 11)
2021-04-01 ftp/jftpgw: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-01 ftp/pureadmin: Unmaintained and dead upstream, does not build with
-fno-common (llvm 11)
2021-04-02 textproc/hs-pandoc-citeproc: Integrated into textproc/hs-pandoc

    5980fd4

08:09 Mathieu Arnold (mat) 

One more small cleanup, forgotten yesterday.
Reported by:	lwhsu

    cf118cc

14:31 Mathieu Arnold (mat) 

Remove # $FreeBSD$ from Makefiles.

    305f148

16:32 jwb 

biology/vcf2hap: Generate .hap file from VCF for haplohseq

vcf2hap is a simple tool for generating a .hap file from a VCF. The .hap file
is required by haplohseq.  vcf2hap is extremely fast and requires a trivial
amount of memory regardless of the size of the VCF file.

 

15:15 jwb 

biology/ad2vcf: Add allelic depth info from a SAM stream to a VCF file

ad2vdf extracts allelic depth info from a SAM stream and adds it to a
corresponding single-sample VCF file.  SAM input is read via stdin and the VCF
input file is taken as a command-line argument. This allows expensive BAM/CRAM
decoding to be performed in parallel by a separate samtools process.

 

15:17 jwb 

biology/vcf-split: Split a multi-sample VCF into single-sample VCFs

Vcf-split splits a multi-sample VCF into single-sample VCFs, writing thousands
of output files simultaneously.  Parsing the TOPMed human chromosome 1 BCF
with bcftools takes two days, so extracting the 137,977 samples one at a time
or using thousands of parallel readers of the same file is impractical.
Vcf-split solves this by generating thousands of single-sample outputs during
a single sweep through the multi-sample input.

 

15:10 jwb 

biology/biolibc: Low-level high-performance bioinformatics library

Biolibc is a library of fast, memory-efficient, low-level functions for
processing biological data.  Like libc, it consists of numerous disparate,
general-purpose functions which could be used by a wide variety of
applications.  These include functions for streaming common file formats such
as SAM and VCF, string functions specific to bioinformatics, etc.

 

20:09 jwb 

biology/generand: Generate random genomic data in FAST[AQ], SAM, or VCF format

Generate random genomic data in FASTA/FASTQ, SAM, or VCF format, suitable for
small academic examples or test inputs of arbitrary size.  Output can be piped
directly to programs or redirected to a file and edited to taste.

 

23:37 yuri 

Move: biology/py-fastTSNE -> math/py-openTSNE

Project was renamed and reimplemented.

 

09:49 yuri 

New port: biology/rampler: Standalone module for sampling genomic sequences

 

09:41 yuri 

New port: biology/edlib: Fast C++ library for sequence alignment using edit
distance

 

09:28 yuri 

New port: biology/spoa: C++ implementation of the partial order alignment (POA)
algorithm

 

09:01 yuri 

New port: biology/biosoup: Collection of C++ header-only data structures for
bioinformatics

 

07:56 yuri 

New port: biology/bioparser: C++ header only parsing library for several formats
in bioinformatics

 

21:44 antoine 

Hook haplohseq to the build

 

18:50 jwb 

biology/pooler: Optimise DNA sequencing primer-set combinations

Optimise combinations of primers and minimise the formation of dimers in
multiplexed PCR.

Primer Pooler can:

* Check through each proposed pool for combinations that are likely to form
  dimers

* Automatically move prospective amplicons between proposed pools to reduce
  dimer formation

* Automatically search the genome sequence to find which amplicons overlap, and
  place their corresponding primers in separate pools

* Optionally keep pool sizes within a specified range

* Handle thousands of primers without being slow (useful for high-throughput
  sequencing applications)

* Do all of the above with degenerate primers too.

WWW: http://ssb22.user.srcf.net/pooler/

PR:             ports/251065
Submitted by:   Silas S. Brown <silas-freebsd@flatline.org.uk>

 

19:31 jrm 

biology/py-biom-format: Restore in preparation for an update to v2.1.8

Version 2.1.8 supports python 3

 

13:01 rene 

Remove expired ports:

2020-09-15 audio/abraca: Uses deprecated version of python
2020-09-15 audio/ardour5: Uses deprecated version of python
2020-09-15 audio/cplay: Uses deprecated version of python
2020-09-15 audio/cpp-xmms2: Uses deprecated version of python
2020-09-15 audio/p5-xmms2: Uses deprecated version of python
2020-09-15 biology/haplohseq: Uses deprecated version of python
2020-09-15 biology/tophat: Uses deprecated version of python
2020-09-15 chinese/ibus-array: Uses deprecated version of python
2020-09-15 comms/congruity: Uses deprecated version of python
2020-09-15 comms/libbtbb: Uses deprecated version of python
2020-09-15 comms/quisk: Uses deprecated version of python
2020-09-15 databases/mtools-mongodb: Uses deprecated version of python
2020-09-15 databases/mydbf2mysql: Uses deprecated version of python

(Only the first 15 lines of the commit message are shown above )