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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.
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non port: biology/Makefile
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Number of commits found XX: 220 (showing only 100 on this page)

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Sat, 13 Jun 2020
[ 13:54 jwb ] Original commit   Revision:538672
538672 biology/Makefile
538672 biology/picard-tools
538672 biology/picard-tools/Makefile
538672 biology/picard-tools/buildlog-12-1-amd64-wip-picard-tools
538672 biology/picard-tools/distinfo
538672 biology/picard-tools/files
538672 biology/picard-tools/files/picard.in
538672 biology/picard-tools/pkg-descr
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.
Fri, 5 Jun 2020
[ 02:45 jwb ] Original commit   Revision:537983
537983 biology/Makefile
537983 biology/bioawk
537983 biology/bioawk/Makefile
537983 biology/bioawk/distinfo
537983 biology/bioawk/files
537983 biology/bioawk/files/patch-Makefile
537983 biology/bioawk/pkg-descr
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   Revision:537982
537982 biology/Makefile
537982 biology/subread
537982 biology/subread/Makefile
537982 biology/subread/distinfo
537982 biology/subread/files
537982 biology/subread/files/Makefile.pkg
537982 biology/subread/files/patch-HelperFunctions.c
537982 biology/subread/files/patch-core-junction.c
537982 biology/subread/files/patch-gene-algorithms.c
537982 biology/subread/files/patch-input-files.c

(Only the first 10 of 20 ports in this commit are shown above. View all ports for this commit)
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   Revision:537926
537926 biology/Makefile
537926 biology/vt
537926 biology/vt/Makefile
537926 biology/vt/distinfo
537926 biology/vt/files
537926 biology/vt/files/patch-Makefile
537926 biology/vt/files/patch-lib_Rmath_Make.inc
537926 biology/vt/files/patch-lib_pcre2_Makefile
537926 biology/vt/files/patch-svm__predict.h
537926 biology/vt/files/patch-svm__train.h

(Only the first 10 of 11 ports in this commit are shown above. View all ports for this commit)
bioloty/vt: Discovers short variants from Next Generation Sequencing data
Sat, 16 May 2020
[ 03:11 yuri ] Original commit   Revision:535347
535347 biology/Makefile
535347 biology/py-hits
535347 biology/py-hits/Makefile
535347 biology/py-hits/distinfo
535347 biology/py-hits/pkg-descr
New port: biology/py-hits: Utilities for processing high-throughput sequencing
experiments
[ 02:25 yuri ] Original commit   Revision:535344
535344 biology/Makefile
535344 biology/py-scikit-bio
535344 biology/py-scikit-bio/Makefile
535344 biology/py-scikit-bio/distinfo
535344 biology/py-scikit-bio/pkg-descr
New port: biology/py-scikit-bio: Data structures, algorithms, educational
resources for bioinformatics
[ 00:14 yuri ] Original commit   Revision:535340
535340 biology/Makefile
535340 biology/py-pandas-charm
535340 biology/py-pandas-charm/Makefile
535340 biology/py-pandas-charm/distinfo
535340 biology/py-pandas-charm/pkg-descr
New port: biology/py-pandas-charm: Library for getting character matrices into
and out of pandas
[ 00:13 yuri ] Original commit   Revision:535339
535339 biology/Makefile
535339 biology/py-ete3
535339 biology/py-ete3/Makefile
535339 biology/py-ete3/distinfo
535339 biology/py-ete3/pkg-descr
New port: biology/py-ete3: Framework for the analysis and visualization of trees
Fri, 15 May 2020
[ 04:58 yuri ] Original commit   Revision:535266
535266 biology/Makefile
535266 biology/scrm
535266 biology/scrm/Makefile
535266 biology/scrm/distinfo
535266 biology/scrm/files
535266 biology/scrm/files/patch-src_random_fastfunc.h
535266 biology/scrm/pkg-descr
New port: biology/scrm: Coalescent simulator for biological sequences
Sun, 10 May 2020
[ 15:42 danfe ] Original commit   Revision:534852
534852 MOVED
534852 biology/Makefile
534852 biology/ugene
534852 biology/ugene/Makefile
534852 biology/ugene/distinfo
534852 biology/ugene/files/patch-git_578c949
534852 biology/ugene/files/patch-src_plugins_test__runner_src_Reporter.ui
534852 biology/ugene/pkg-plist
- Resurrect and unbreak by updating to version 34.0
- Stop providing outdated offline PDF documentation,
  users are advised to use the online files instead
Tue, 5 May 2020
[ 15:38 rene ] Original commit   Revision:534093
534093 LEGAL
534093 MOVED
534093 audio/Makefile
534093 audio/festvox-czech
534093 audio/gkrellmvolume2
534093 audio/mixmos
534093 audio/mma
534093 audio/pd-cyclone
534093 audio/shorten
534093 audio/taglib-sharp

(Only the first 10 of 492 ports in this commit are shown above. View all ports for this commit)
Remove expired ports:

Adjusted for ports rescued since r534032

2020-05-05 audio/festvox-czech: Broken for more than 6 months
2020-05-05 audio/gkrellmvolume2: Broken for more than 6 months
2020-05-05 audio/mixmos: Broken for more than 6 months
2020-05-05 audio/mma: Broken for more than 6 months
2020-05-05 audio/pd-cyclone: Broken for more than 6 months
2020-05-05 audio/shorten: Broken for more than 6 months
2020-05-05 audio/taglib-sharp: Broken for more than 6 months
2020-05-05 audio/xhippo: Broken for more than 6 months
2020-05-05 biology/consed: Broken for more than 6 months
2020-05-05 biology/plinkseq: Broken for more than 6 months
2020-05-05 biology/seqtools: Broken for more than 6 months
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Mon, 4 May 2020
[ 23:01 jwb ] Original commit   Revision:533993
533993 biology/Makefile
533993 biology/plink
533993 biology/plink/Makefile
533993 biology/plink/distinfo
533993 biology/plink/files/patch-Makefile
533993 biology/plink/files/patch-elf.cpp
533993 biology/plink/files/patch-idhelp.cpp
533993 biology/plink/files/patch-plink__common.h
533993 biology/plink/files/patch-sets.cpp
533993 biology/plink/pkg-descr

(Only the first 10 of 11 ports in this commit are shown above. View all ports for this commit)
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
Wed, 15 Apr 2020
[ 15:22 jwb ] Original commit   Revision:531770
531770 biology/Makefile
531770 biology/gcta
531770 biology/gcta/Makefile
531770 biology/gcta/distinfo
531770 biology/gcta/files
531770 biology/gcta/files/patch-Makefile
531770 biology/gcta/files/patch-eigen__func.h
531770 biology/gcta/files/patch-gcta.h
531770 biology/gcta/files/patch-ld.cpp
531770 biology/gcta/files/patch-mkl.cpp

(Only the first 10 of 11 ports in this commit are shown above. View all ports for this commit)
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.
Sat, 21 Mar 2020
[ 23:03 0mp ] Original commit   Revision:528886
528886 GIDs
528886 LEGAL
528886 MOVED
528886 UIDs
528886 biology/Makefile
528886 biology/linux-foldingathome
528886 biology/linux-foldingathome/Makefile
528886 biology/linux-foldingathome/distinfo
528886 biology/linux-foldingathome/files
528886 biology/linux-foldingathome/files/fahclient.in

(Only the first 10 of 13 ports in this commit are shown above. View all ports for this commit)
Resurrect biology/linux-foldingathome

Special thanks to netchild for inspiring bringing back this piece software
to ports!

Reviewed by:	netchild, pi, salvadore
Differential Revision:	https://reviews.freebsd.org/D24127
Mon, 27 Jan 2020
[ 15:34 rene ] Original commit   Revision:524263
524263 LEGAL
524263 MOVED
524263 accessibility/Makefile
524263 accessibility/py-papi
524263 archivers/Makefile
524263 archivers/py-czipfile
524263 audio/Makefile
524263 audio/boodler
524263 audio/dir2ogg
524263 audio/jokosher

(Only the first 10 of 220 ports in this commit are shown above. View all ports for this commit)
Remove expired ports:

2020-01-27 accessibility/py-papi: Unmaintained, uses EOLed python27
2020-01-27 archivers/py-czipfile: Unmaintained, uses EOLed python27
2020-01-27 audio/boodler: Unmaintained, uses EOLed python27
2020-01-27 audio/dir2ogg: Unmaintained, uses EOLed python27
2020-01-27 audio/jokosher: Unmaintained, uses EOLed python27
2020-01-27 audio/mpdbrowser: Unmaintained, uses EOLed python27
2020-01-27 audio/nekobee: Unmaintained, uses EOLed python27
2020-01-27 audio/patchage: Unmaintained, uses EOLed python27
2020-01-27 audio/py-ao: Unmaintained, uses EOLed python27
2020-01-27 audio/py-id3: Unmaintained, uses EOLed python27
2020-01-27 audio/py-shout: Unmaintained, uses EOLed python27
2020-01-27 audio/py-speex: Unmaintained, uses EOLed python27
2020-01-27 audio/pytone: Unmaintained, uses EOLed python27
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Sun, 8 Dec 2019
[ 16:49 sunpoet ] Original commit   Revision:519320
519320 biology/Makefile
519320 biology/p5-Bio-Variation
519320 biology/p5-Bio-Variation/Makefile
519320 biology/p5-Bio-Variation/distinfo
519320 biology/p5-Bio-Variation/pkg-descr
519320 biology/p5-Bio-Variation/pkg-plist
Add p5-Bio-Variation 1.7.4

Bio::Variation::* provides BioPerl variation-related functionality.

WWW: https://metacpan.org/release/Bio-Variation
[ 16:49 sunpoet ] Original commit   Revision:519319
519319 biology/Makefile
519319 biology/p5-Bio-DB-NCBIHelper
519319 biology/p5-Bio-DB-NCBIHelper/Makefile
519319 biology/p5-Bio-DB-NCBIHelper/distinfo
519319 biology/p5-Bio-DB-NCBIHelper/pkg-descr
519319 biology/p5-Bio-DB-NCBIHelper/pkg-plist
Add p5-Bio-DB-NCBIHelper 1.7.6

Bio::DB::NCBIHelper provides a single place to setup some common methods for
querying NCBI web databases. This module just centralizes the methods for
constructing a URL for querying NCBI GenBank and NCBI GenPept and the common
HTML stripping done in postprocess_data().

WWW: https://metacpan.org/release/Bio-DB-NCBIHelper
[ 16:49 sunpoet ] Original commit   Revision:519318
519318 biology/Makefile
519318 biology/p5-Bio-DB-EMBL
519318 biology/p5-Bio-DB-EMBL/Makefile
519318 biology/p5-Bio-DB-EMBL/distinfo
519318 biology/p5-Bio-DB-EMBL/pkg-descr
519318 biology/p5-Bio-DB-EMBL/pkg-plist
Add p5-Bio-DB-EMBL 1.7.4

Bio::DB::EMBL allows the dynamic retrieval of sequence objects Bio::Seq from the
EMBL database using the dbfetch script at EBI.

In order to make changes transparent we have host type (currently only ebi) and
location (defaults to ebi) separated out. This allows later additions of more
servers in different geographical locations.

The functionality of this module is inherited from Bio::DB::DBFetch which
implements Bio::DB::WebDBSeqI.

WWW: https://metacpan.org/release/Bio-DB-EMBL
Wed, 16 Oct 2019
[ 15:29 rene ] Original commit   Revision:514601
514601 LEGAL
514601 MOVED
514601 archivers/Makefile
514601 archivers/freetar
514601 archivers/hffzip
514601 archivers/hpack.non-usa.only
514601 archivers/untar
514601 astro/Makefile
514601 astro/gpsdrive
514601 astro/planets

(Only the first 10 of 369 ports in this commit are shown above. View all ports for this commit)
Remove expired ports:

2019-10-16 archivers/freetar: Unfetchable, unmaintained
2019-10-16 archivers/hffzip: Unfetchable, unmaintained
2019-10-16 archivers/hpack.non-usa.only: Unfetchable, unmaintained
2019-10-16 archivers/untar: Unfetchable, unmaintained
2019-10-16 astro/gpsdrive: Unfetchable, unmaintained
2019-10-16 astro/planets: Unfetchable, unmaintained
2019-10-16 audio/ascd: Unfetchable, unmaintained
2019-10-16 audio/audiotag: Unfetchable, unmaintained
2019-10-16 audio/gmidimonitor: Unfetchable, unmaintained
2019-10-16 audio/gmpc-lyricwiki: Unfetchable, unmaintained
2019-10-16 audio/jack_mixer: Unfetchable, unmaintained
2019-10-16 audio/jmusic: Unfetchable, unmaintained
2019-10-16 audio/maplay: Unfetchable, unmaintained
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Fri, 27 Sep 2019
[ 00:49 jwb ] Original commit   Revision:512997
512997 biology/Makefile
512997 biology/tophat
512997 biology/tophat/Makefile
512997 biology/tophat/distinfo
512997 biology/tophat/files
512997 biology/tophat/files/patch-configure
512997 biology/tophat/files/patch-src-samtools-0.1.18-Makefile
512997 biology/tophat/files/patch-src_Makefile.in
512997 biology/tophat/files/tophat-test
512997 biology/tophat/pkg-descr

(Only the first 10 of 11 ports in this commit are shown above. View all ports for this commit)
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   Revision:512646
512646 biology/Makefile
512646 biology/py-multiqc
512646 biology/py-multiqc/Makefile
512646 biology/py-multiqc/distinfo
512646 biology/py-multiqc/files
512646 biology/py-multiqc/files/patch-multiqc_utils_config.py
512646 biology/py-multiqc/files/patch-scripts_multiqc
512646 biology/py-multiqc/pkg-descr
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.
Mon, 16 Sep 2019
[ 01:07 jwb ] Original commit   Revision:512137
512137 biology/Makefile
512137 biology/haplohseq
512137 biology/haplohseq/Makefile
512137 biology/haplohseq/distinfo
512137 biology/haplohseq/files
512137 biology/haplohseq/files/patch-makefile
512137 biology/haplohseq/files/patch-src_HaplohSeq.cpp
512137 biology/haplohseq/files/patch-src_test_InputProcessorTest.cpp
512137 biology/haplohseq/files/run-tests
512137 biology/haplohseq/pkg-descr
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.
Thu, 11 Jul 2019
[ 17:05 yuri ] Original commit   Revision:506417
506417 biology/Makefile
506417 biology/libbigwig
506417 biology/libbigwig/Makefile
506417 biology/libbigwig/distinfo
506417 biology/libbigwig/files
506417 biology/libbigwig/files/patch-Makefile
506417 biology/libbigwig/pkg-descr
New port: biology/libbigwig: C library for handling bigWig files (containing
genomic data)
Mon, 24 Jun 2019
[ 09:29 yuri ] Original commit   Revision:505017
505017 biology/Makefile
505017 biology/viennarna
505017 biology/viennarna/Makefile
505017 biology/viennarna/distinfo
505017 biology/viennarna/files
505017 biology/viennarna/files/patch-RNA-Tutorial_Makefile.in
505017 biology/viennarna/files/patch-configure
505017 biology/viennarna/files/patch-examples_Makefile.in
505017 biology/viennarna/files/patch-src_bin_Makefile.in
505017 biology/viennarna/pkg-descr

(Only the first 10 of 11 ports in this commit are shown above. View all ports for this commit)
New port: biology/viennarna: Alignment tools for the structural analysis of RNA
Sat, 15 Jun 2019
[ 20:37 yuri ] Original commit   Revision:504268
504268 biology/Makefile
504268 biology/treekin
504268 biology/treekin/Makefile
504268 biology/treekin/distinfo
504268 biology/treekin/pkg-descr
New port: biology/treekin: Efficient computation of RNA folding dynamics
Sun, 26 May 2019
[ 03:36 jwb ] Original commit   Revision:502673
502673 biology/Makefile
502673 biology/bolt-lmm
502673 biology/bolt-lmm/Makefile
502673 biology/bolt-lmm/distinfo
502673 biology/bolt-lmm/files
502673 biology/bolt-lmm/files/patch-example_run__example.sh
502673 biology/bolt-lmm/files/patch-example_run__example__reml2.sh
502673 biology/bolt-lmm/files/patch-src_Makefile
502673 biology/bolt-lmm/files/patch-src_StringUtils.cpp
502673 biology/bolt-lmm/pkg-descr

(Only the first 10 of 11 ports in this commit are shown above. View all ports for this commit)
biology/bolt-lmm: Mixed model association testing and variance component
analysis

The BOLT-LMM software package currently consists of two main algorithms, the
BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML
algorithm for variance components analysis (i.e., partitioning of
SNP-heritability and estimation of genetic correlations).
Sat, 25 May 2019
[ 22:28 yuri ] Original commit   Revision:502661
502661 biology/Makefile
502661 biology/cufflinks
502661 biology/cufflinks/Makefile
502661 biology/cufflinks/distinfo
502661 biology/cufflinks/files
502661 biology/cufflinks/files/patch-src_GBase.h
502661 biology/cufflinks/files/patch-src_biascorrection.h
502661 biology/cufflinks/pkg-descr
New port: biology/cufflinks: Cufflinks assembles transcripts, estimates their
abundance, etc
Mon, 20 May 2019
[ 17:59 yuri ] Original commit   Revision:502128
502128 biology/Makefile
502128 biology/mothur
502128 biology/mothur/Makefile
502128 biology/mothur/distinfo
502128 biology/mothur/pkg-descr
New port: biology/mothur: Software for bioinformatics of the microbial ecology
community
Sun, 19 May 2019
[ 06:52 yuri ] Original commit   Revision:502015
502015 biology/Makefile
502015 biology/hhsuite
502015 biology/hhsuite/Makefile
502015 biology/hhsuite/distinfo
502015 biology/hhsuite/files
502015 biology/hhsuite/files/patch-data_CMakeLists.txt
502015 biology/hhsuite/files/patch-scripts_CMakeLists.txt
502015 biology/hhsuite/files/patch-src_cs_getopt__pp.cc
502015 biology/hhsuite/pkg-descr
502015 biology/hhsuite/pkg-plist
New port: biology/hhsuite: Remote protein homology detection suite
Fri, 17 May 2019
[ 14:45 jwb ] Original commit   Revision:501873
501873 biology/Makefile
501873 biology/gemma
501873 biology/gemma/Makefile
501873 biology/gemma/distinfo
501873 biology/gemma/files
501873 biology/gemma/files/Makefile
501873 biology/gemma/files/patch-doc_manual.tex
501873 biology/gemma/files/patch-src_gemma.cpp
501873 biology/gemma/pkg-descr
501873 biology/gemma/pkg-plist
biology/gemma: Genome-wide Efficient Mixed Model Association

GEMMA is a software toolkit for fast application of linear mixed models (LMMs)
and related models to genome-wide association studies (GWAS) and other
large-scale data sets.
Thu, 9 May 2019
[ 21:28 jwb ] Original commit   Revision:501147
501147 biology/Makefile
501147 biology/vsearch
501147 biology/vsearch/Makefile
501147 biology/vsearch/distinfo
501147 biology/vsearch/files
501147 biology/vsearch/files/patch-configure.ac
501147 biology/vsearch/files/patch-src_Makefile.am
501147 biology/vsearch/files/patch-src_city.cc
501147 biology/vsearch/files/patch-src_vsearch.h
501147 biology/vsearch/pkg-descr
biology/vsearch: Versatile open-source tool for metagenomics

VSEARCH supports de novo and reference based chimera detection, clustering,
full-length and prefix dereplication, rereplication, reverse complementation,
masking, all-vs-all pairwise global alignment, exact and global alignment
searching, shuffling, subsampling and sorting. It also supports FASTQ file
analysis, filtering, conversion and merging of paired-end reads.

The aim of this project is to create an alternative to the USEARCH tool
developed by Robert C. Edgar (2010).
Fri, 3 May 2019
[ 14:41 jwb ] Original commit   Revision:500737
500737 biology/Makefile
500737 biology/fastp
500737 biology/fastp/Makefile
500737 biology/fastp/distinfo
500737 biology/fastp/files
500737 biology/fastp/files/patch-Makefile
500737 biology/fastp/pkg-descr
biology/fastp: Ultra-fast all-in-one FASTQ preprocessor

fastp is a tool designed to provide fast all-in-one preprocessing for FastQ
files. This tool is developed in C++ with multithreading supported to afford
high performance.
Wed, 24 Apr 2019
[ 18:03 jwb ] Original commit   Revision:499895
499895 biology/Makefile
499895 biology/minimap2
499895 biology/minimap2/Makefile
499895 biology/minimap2/distinfo
499895 biology/minimap2/files
499895 biology/minimap2/files/patch-Makefile
499895 biology/minimap2/pkg-descr
biology/minimap2: Pairwise aligner for genomic and spliced nucleotide sequences

Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA
sequences against a large reference database.
Sun, 21 Apr 2019
[ 20:30 jwb ] Original commit   Revision:499592
499592 biology/Makefile
499592 biology/star
499592 biology/star/Makefile
499592 biology/star/distinfo
499592 biology/star/files
499592 biology/star/files/patch-Makefile
499592 biology/star/files/patch-SharedMemory.cpp
499592 biology/star/pkg-descr
biology/star: Spliced Transcripts Alignment to a Reference

STAR is an extremely fast RNA-seq aligner, an alternative to tophat2,
hisat2, bowtie, subread, etc.
Fri, 12 Apr 2019
[ 17:01 yuri ] Original commit   Revision:498729
498729 biology/Makefile
498729 biology/py-xenaPython
498729 biology/py-xenaPython/Makefile
498729 biology/py-xenaPython/distinfo
498729 biology/py-xenaPython/pkg-descr
New port: biology/py-xenaPython: API for Xena Hub to access genetic information
shared through the hub
Sun, 24 Mar 2019
[ 19:40 jwb ] Original commit   Revision:496770
496770 biology/Makefile
496770 biology/py-dnaio
496770 biology/py-dnaio/Makefile
496770 biology/py-dnaio/distinfo
496770 biology/py-dnaio/pkg-descr
biology/py-dnaio: Read and write FASTQ and FASTA

Factored out of py-cutadapt

Reviewed by:    jrm
Sat, 16 Mar 2019
[ 21:55 tcberner ] Original commit   Revision:495967
495967 MOVED
495967 accessibility/Makefile
495967 accessibility/qt4-accessible
495967 astro/Makefile
495967 astro/qlandkartegt
495967 astro/stellarium-qt4
495967 astro/xglobe
495967 audio/Makefile
495967 audio/acoustid-fingerprinter
495967 audio/cueplayer

(Only the first 10 of 315 ports in this commit are shown above. View all ports for this commit)
Qt4 deprecation: Remove Qt4 and its consumes.

2019-03-15 accessibility/qt4-accessible: Qt4 has been EOL since december 2015
2019-03-15 astro/qlandkartegt: Qt4 has been EOL since december 2015
2019-03-15 astro/stellarium-qt4: Qt4 has been EOL since december 2015
2019-03-15 astro/xglobe: Qt4 has been EOL since december 2015
2019-03-15 audio/acoustid-fingerprinter: Qt4 has been EOL since december 2015
2019-03-15 audio/cueplayer: Qt4 has been EOL since december 2015
2019-03-15 audio/esperanza: Qt4 has been EOL since december 2015
2019-03-15 audio/lastfm-desktop: Qt4 has been EOL since december 2015
2019-03-15 audio/minitunes: Qt4 has been EOL since december 2015
2019-03-15 audio/mixxx20: Qt4 has been EOL since december 2015
2019-03-15 audio/mumble: Qt4 has been EOL since december 2015
2019-03-15 audio/murmur: Qt4 has been EOL since december 2015
2019-03-15 audio/puddletag: Qt4 has been EOL since december 2015
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Mon, 25 Feb 2019
[ 07:56 yuri ] Original commit   Revision:493842
493842 biology/Makefile
493842 biology/abyss
493842 biology/abyss/Makefile
493842 biology/abyss/distinfo
493842 biology/abyss/files
493842 biology/abyss/files/patch-Common_Timer.h
493842 biology/abyss/pkg-descr
493842 biology/abyss/pkg-plist
New port: biology/abyss: Assembly By Short Sequences: parallel, paired-end
sequence assembler
Wed, 20 Feb 2019
[ 20:46 sunpoet ] Original commit   Revision:493444
493444 biology/Makefile
493444 biology/p5-Bio-Cluster
493444 biology/p5-Bio-Cluster/Makefile
493444 biology/p5-Bio-Cluster/distinfo
493444 biology/p5-Bio-Cluster/pkg-descr
493444 biology/p5-Bio-Cluster/pkg-plist
Add p5-Bio-Cluster 1.7.3

Bio::Cluster is the BioPerl cluster modules. Classes and modules here describe
the basic structure for a cluster of BioPerl objects.

WWW: https://metacpan.org/release/Bio-Cluster
Sun, 3 Feb 2019
[ 21:14 yuri ] Original commit   Revision:492079
492079 biology/Makefile
492079 biology/figtree
492079 biology/figtree/Makefile
492079 biology/figtree/distinfo
492079 biology/figtree/pkg-descr
New port: biology/figtree: Graphical viewer of phylogenetic trees
[ 20:13 yuri ] Original commit   Revision:492071
492071 biology/Makefile
492071 biology/graphlan
492071 biology/graphlan/Makefile
492071 biology/graphlan/distinfo
492071 biology/graphlan/pkg-descr
492071 biology/graphlan/pkg-plist
New port: biology/graphlan: High-quality circular representations of taxonomic,
phylogenetic trees
[ 18:49 yuri ] Original commit   Revision:492059
492059 biology/Makefile
492059 biology/prodigy-lig
492059 biology/prodigy-lig/Makefile
492059 biology/prodigy-lig/distinfo
492059 biology/prodigy-lig/pkg-descr
New port: biology/prodigy-lig: Prediction of protein-small molecule binding
affinities
[ 18:08 yuri ] Original commit   Revision:492058
492058 biology/Makefile
492058 biology/prodigal
492058 biology/prodigal/Makefile
492058 biology/prodigal/distinfo
492058 biology/prodigal/pkg-descr
New port: biology/prodigal: Protein-coding gene prediction for prokaryotic
genomes
Tue, 29 Jan 2019
[ 07:56 yuri ] Original commit   Revision:491546
491546 biology/Makefile
491546 biology/dsr-pdb
491546 biology/dsr-pdb/Makefile
491546 biology/dsr-pdb/distinfo
491546 biology/dsr-pdb/files
491546 biology/dsr-pdb/files/patch-Makefile.in
491546 biology/dsr-pdb/files/patch-include_dsrpdb_geometry__internal.h
491546 biology/dsr-pdb/files/patch-lib_PDB.cc
491546 biology/dsr-pdb/files/patch-tools_pdb__align__points.cc
491546 biology/dsr-pdb/pkg-descr

(Only the first 10 of 11 ports in this commit are shown above. View all ports for this commit)
New port: biology/dsr-pdb: Simple C++ PDB reader (reads the protein description
format)
Tue, 22 Jan 2019
[ 16:26 mat ] Original commit   Revision:490961
490961 biology/Makefile
490961 databases/Makefile
490961 deskutils/Makefile
490961 devel/Makefile
490961 graphics/Makefile
490961 math/Makefile
490961 net/Makefile
490961 science/Makefile
490961 sysutils/Makefile
490961 www/Makefile
Sort categories Makefiles.
Fri, 11 Jan 2019
[ 16:02 jwb ] Original commit   Revision:489981
489981 biology/Makefile
489981 biology/hisat2
489981 biology/hisat2/Makefile
489981 biology/hisat2/distinfo
489981 biology/hisat2/files
489981 biology/hisat2/files/Makefile.pkg
489981 biology/hisat2/files/patch-hisat2
489981 biology/hisat2/pkg-descr
489981 biology/hisat2/pkg-plist
New port: biology/hisat2: Program for mapping next-generation sequencing reads

Approved by:    jrm (mentor, implicit)
Fri, 21 Dec 2018
[ 13:19 rene ] Original commit   Revision:487992
487992 MOVED
487992 audio/Makefile
487992 audio/gkrellmms2
487992 audio/gmixer
487992 audio/gqmpeg
487992 audio/mcplay
487992 audio/rio500
487992 audio/scrobbler
487992 audio/soundtracker
487992 audio/wmalbum

(Only the first 10 of 140 ports in this commit are shown above. View all ports for this commit)
Remove expired ports:
2018-12-19 net/py-libstorj: Broken for more than 6 months
2018-12-20 net/xferstats: Uses obsolete glib12
2018-12-20 net/wmlj: Uses obsolete glib12
2018-12-20 net/ipsorc: Uses obsolete glib12
2018-12-20 net/bsdproxy: Uses obsolete glib12
2018-12-20 net/gini: Uses obsolete glib12
2018-12-21 net/netatalk: Outdated branch of netatalk; use net/netatalk3 instead
2018-12-20 net/nocatsplash: Uses obsolete glib12
2018-12-20 net/jags: Uses obsolete glib12
2018-12-19 net/scribe: Broken for more than 6 months
2018-12-20 net/libnetdude: Uses obsolete glib12
2018-12-20 net/nepim: Uses obsolete glib12
2018-12-20 emulators/generator: Uses obsolete glib12
2018-12-19 emulators/py-nova: Broken for more than 6 months
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Sat, 15 Dec 2018
[ 08:58 yuri ] Original commit   Revision:487491
487491 biology/Makefile
487491 biology/py-fastTSNE
487491 biology/py-fastTSNE/Makefile
487491 biology/py-fastTSNE/distinfo
487491 biology/py-fastTSNE/files
487491 biology/py-fastTSNE/files/patch-setup.py
487491 biology/py-fastTSNE/pkg-descr
New port: biology/py-fastTSNE: Fast, parallel implementations of t-SNE
Tue, 11 Dec 2018
[ 15:04 jrm ] Original commit   Revision:487239
487239 MOVED
487239 biology/Makefile
487239 biology/njplot
Remove biology/njplot

The author of both NJplot and SeaView says that NJplot can be considered
deprecated and replaced by SeaView.
Fri, 7 Dec 2018
[ 00:26 yuri ] Original commit   Revision:486814
486814 biology/Makefile
486814 biology/checkm
486814 biology/checkm/Makefile
486814 biology/checkm/distinfo
486814 biology/checkm/pkg-descr
New port: math/checkm: Quality assessment tool for the microbial genomes
[ 00:10 yuri ] Original commit   Revision:486812
486812 biology/Makefile
486812 biology/groopm
486812 biology/groopm/Makefile
486812 biology/groopm/distinfo
486812 biology/groopm/pkg-descr
New port: math/groopm: Metagenomic binning suite
Mon, 3 Dec 2018
[ 08:40 yuri ] Original commit   Revision:486502
486502 biology/Makefile
486502 biology/gatk
486502 biology/gatk/Makefile
486502 biology/gatk/distinfo
486502 biology/gatk/files
486502 biology/gatk/files/gatk.sh.in
486502 biology/gatk/files/patch-build.gradle
486502 biology/gatk/pkg-descr
New port: biology/gatk: Variant discovery in high-throughput sequencing data
Fri, 19 Oct 2018
[ 02:06 yuri ] Original commit   Revision:482400
482400 biology/Makefile
482400 biology/py-gffutils
482400 biology/py-gffutils/Makefile
482400 biology/py-gffutils/distinfo
482400 biology/py-gffutils/pkg-descr
New port: biology/py-gffutils: Work with GFF and GTF files in a flexible
database framework
[ 02:05 yuri ] Original commit   Revision:482399
482399 biology/Makefile
482399 biology/py-pyfaidx
482399 biology/py-pyfaidx/Makefile
482399 biology/py-pyfaidx/distinfo
482399 biology/py-pyfaidx/pkg-descr
New port: biology/py-pyfaidx: Efficient pythonic random access to fasta
subsequences
[ 02:03 yuri ] Original commit   Revision:482398
482398 biology/Makefile
482398 biology/py-gtfparse
482398 biology/py-gtfparse/Makefile
482398 biology/py-gtfparse/distinfo
482398 biology/py-gtfparse/pkg-descr
New port: biology/py-gtfparse: Parsing tools for GTF (gene transfer format)
files
Mon, 8 Oct 2018
[ 07:54 yuri ] Original commit   Revision:481520
481520 biology/Makefile
481520 biology/ncbi-cxx-toolkit
481520 biology/ncbi-cxx-toolkit/Makefile
481520 biology/ncbi-cxx-toolkit/distinfo
481520 biology/ncbi-cxx-toolkit/files
481520 biology/ncbi-cxx-toolkit/files/patch-src_build-system_Makefile.in.top
481520 biology/ncbi-cxx-toolkit/pkg-descr
New port: biology/ncbi-cxx-toolkit: NCBI C++ Toolkit
Sun, 7 Oct 2018
[ 00:19 yuri ] Original commit   Revision:481406
481406 MOVED
481406 biology/Makefile
481406 biology/tinker
481406 science/Makefile
481406 science/tinker
481406 science/tinker/Makefile
481406 science/tinker/distinfo
481406 science/tinker/files/patch-bench__bench1.run
481406 science/tinker/files/patch-bench__bench2.run
481406 science/tinker/files/patch-bench__bench3.run

(Only the first 10 of 16 ports in this commit are shown above. View all ports for this commit)
biology/tinker: Update 7.1.3 -> 8.4.4; Move to science/

Port changes:
* Take maintainership
* Implement the 'benchmarks' target, and stop installing benchmarks
* Add USES=gmake
* Update license
* Change MASTER_SITES and WWW to https
* Silence some commands
Fri, 21 Sep 2018
[ 08:04 yuri ] Original commit   Revision:480236
480236 biology/Makefile
480236 biology/py-loompy
480236 biology/py-loompy/Makefile
480236 biology/py-loompy/distinfo
480236 biology/py-loompy/pkg-descr
New port: biology/py-loompy: Work with .loom files for single-cell RNA-seq data
Thu, 16 Aug 2018
[ 20:28 rene ] Original commit   Revision:477371
477371 MOVED
477371 biology/Makefile
477371 biology/blat
477371 converters/Makefile
477371 converters/uudx
477371 databases/Makefile
477371 databases/dbf2mysql
477371 devel/Makefile
477371 devel/as31
477371 devel/gdbmods

(Only the first 10 of 45 ports in this commit are shown above. View all ports for this commit)
Remove expired ports:
2018-08-16 net/traceroute: Upstream gone
2018-08-15 net/e169-stats: unknown license
2018-08-15 net/l4ip: unknown license
2018-08-15 net/dhcprelay: unknown license
2018-08-15 emulators/m2000: unknown license
2018-08-15 textproc/ant-xinclude-task: unknown license
2018-08-15 textproc/bomstrip: unknown license
2018-08-15 x11-fonts/ecofont: unknown license
2018-08-15 mail/roundcube-groupvice: unknown license
2018-08-15 security/pft: unknown license
2018-08-15 devel/kickassembler: unknown license
2018-08-15 devel/gdbmods: unknown license
2018-08-15 devel/as31: unknown license
2018-08-15 databases/dbf2mysql: unknown license
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Wed, 8 Aug 2018
[ 12:26 mat ] Original commit   Revision:476639
476639 biology/Makefile
476639 converters/Makefile
476639 databases/Makefile
476639 graphics/Makefile
476639 lang/Makefile
476639 mail/Makefile
476639 math/Makefile
476639 misc/Makefile
476639 multimedia/Makefile
476639 net-mgmt/Makefile

(Only the first 10 of 17 ports in this commit are shown above. View all ports for this commit)
Regular sorting of categories Makefiles.

Sponsored by:	Absolight
Tue, 7 Aug 2018
[ 07:50 yuri ] Original commit   Revision:476578
476578 biology/Makefile
476578 biology/py-orange3-single-cell
476578 biology/py-orange3-single-cell/Makefile
476578 biology/py-orange3-single-cell/distinfo
476578 biology/py-orange3-single-cell/pkg-descr
New port: biology/py-orange3-single-cell: Orange add-on for gene expression of
single cell data
Fri, 13 Jul 2018
[ 07:02 yuri ] Original commit   Revision:474558
474558 biology/Makefile
474558 biology/exonerate
474558 biology/exonerate/Makefile
474558 biology/exonerate/distinfo
474558 biology/exonerate/pkg-descr
474558 biology/exonerate/pkg-plist
New port: biology/exonerate: Generic tool for sequence alignment

PR:		229180
Submitted by:	Motomichi Matsuzaki <mzaki@niid.go.jp>
Wed, 11 Jul 2018
[ 21:32 yuri ] Original commit   Revision:474480
474480 biology/Makefile
474480 biology/stringtie
474480 biology/stringtie/Makefile
474480 biology/stringtie/distinfo
474480 biology/stringtie/files
474480 biology/stringtie/files/patch-Makefile
474480 biology/stringtie/files/patch-gclib_GIntHash.hh
474480 biology/stringtie/files/patch-samtools-0.1.18_Makefile
474480 biology/stringtie/files/patch-samtools-0.1.18_bam__aux.c
474480 biology/stringtie/pkg-descr
New port: biology/stringtie: Transcript assembly and quantification for RNA-seq

PR:		229480
Submitted by:	Motomichi Matsuzaki <mzaki@niid.go.jp>
Tue, 3 Jul 2018
[ 08:42 yuri ] Original commit   Revision:473806
473806 biology/Makefile
473806 biology/cytoscape
473806 biology/cytoscape/Makefile
473806 biology/cytoscape/distinfo
473806 biology/cytoscape/pkg-descr
New port: biology/cytoscape: Software to visualize molecular interaction
networks, gene expression
Mon, 25 Jun 2018
[ 23:56 yuri ] Original commit   Revision:473356
473356 biology/Makefile
473356 biology/igv
473356 biology/igv/Makefile
473356 biology/igv/distinfo
473356 biology/igv/files
473356 biology/igv/files/igv.sh.in
473356 biology/igv/files/patch-build.xml
473356 biology/igv/pkg-descr
New port: biology/igv: Visualization tool for genomic datasets
Thu, 14 Jun 2018
[ 06:25 yuri ] Original commit   Revision:472358
472358 biology/Makefile
472358 biology/py-orange3-bioinformatics
472358 biology/py-orange3-bioinformatics/Makefile
472358 biology/py-orange3-bioinformatics/distinfo
472358 biology/py-orange3-bioinformatics/pkg-descr
New port: biology/py-orange3-bioinformatics: Orange add-on providing common
functionality for bioinformatics
Wed, 13 Jun 2018
[ 01:46 yuri ] Original commit   Revision:472277
472277 biology/Makefile
472277 biology/py-Genesis-PyAPI
472277 biology/py-Genesis-PyAPI/Makefile
472277 biology/py-Genesis-PyAPI/distinfo
472277 biology/py-Genesis-PyAPI/pkg-descr
New port: biology/py-Genesis-PyAPI: API for the Genesis platform for genetics
information processing
Sun, 10 Jun 2018
[ 23:58 yuri ] Original commit   Revision:472158
472158 biology/Makefile
472158 biology/ngs-sdk
472158 biology/ngs-sdk/Makefile
472158 biology/ngs-sdk/distinfo
472158 biology/ngs-sdk/files
472158 biology/ngs-sdk/files/patch-Makefile
472158 biology/ngs-sdk/files/patch-configure
472158 biology/ngs-sdk/files/patch-ngs-sdk_setup_install.perl
472158 biology/ngs-sdk/files/patch-ngs-sdk_setup_konfigure.perl
472158 biology/ngs-sdk/pkg-descr

(Only the first 10 of 11 ports in this commit are shown above. View all ports for this commit)
New port: biology/ngs-sdk: Tools and libraries for using data in the INSDC
Sequence Read Archives
Thu, 7 Jun 2018
[ 00:34 rene ] Original commit   Revision:471892
471892 LEGAL
471892 MOVED
471892 audio/Makefile
471892 audio/abcmidi
471892 audio/deforaos-mixer
471892 audio/gkrellmss2
471892 audio/jxm
471892 audio/kaudiocreator
471892 audio/linux-genpuid
471892 audio/ogg2mp3

(Only the first 10 of 51 ports in this commit are shown above. View all ports for this commit)
Remove expired ports:
2018-06-06 biology/ssaha: Broken for more than 6 months
2018-06-06 biology/crux: Broken for more than 6 months
2018-06-06 biology/ariadne: Broken for more than 6 months
2018-06-06 cad/sceptre: Broken for more than 6 months
2018-06-06 cad/cider: Broken for more than 6 months
2018-06-06 chinese/scim-array: Broken for more than 6 months
2018-06-06 chinese/xpdf: Broken for more than 6 months
2018-06-06 chinese/telnet: Broken for more than 6 months
2018-06-06 comms/java-commapi-freebsd: Depends on BROKEN and expiring
comms/java-commapi
2018-06-06 comms/soundmodem: Broken for more than 6 months
2018-06-06 comms/jsdr: Broken for more than 6 months
2018-06-06 comms/java-commapi: Broken for more than 6 months
2018-06-06 converters/pdf2djvu: Broken for more than 6 months
2018-06-06 databases/rdb: Broken for more than 6 months
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Wed, 6 Jun 2018
[ 15:15 krion ] Original commit   Revision:471850
471850 biology/Makefile
471850 biology/infernal
471850 biology/infernal/Makefile
471850 biology/infernal/distinfo
471850 biology/infernal/files
471850 biology/infernal/files/patch-configure
471850 biology/infernal/pkg-descr
471850 biology/infernal/pkg-plist
Add new port: biology/infernal

Infernal is a tool for searching DNA sequence database for RNA
structure and sequence similarities. The Rfam database of RNA
families is based on Infernal, and we can search DNA sequences for
structural homologs of Rfam families.

WWW: http://eddylab.org/infernal/

PR:		228776
Submitted by:	Motomichi Matsuzaki <mzaki@niid.go.jp>
Mon, 21 May 2018
[ 22:15 jwb ] Original commit   Revision:470582
470582 biology/Makefile
470582 biology/clustal-omega
470582 biology/clustal-omega/Makefile
470582 biology/clustal-omega/distinfo
470582 biology/clustal-omega/pkg-descr
470582 biology/clustal-omega/pkg-plist
biology/clustal-omega: Multiple alignment of nucleic acid and protein, replaces
clustalw

Approved by:    jrm
Differential Revision:  https://reviews.freebsd.org/D15516
[ 20:56 jwb ] Original commit   Revision:470575
470575 biology/Makefile
470575 biology/clustalx
470575 biology/clustalx/Makefile
470575 biology/clustalx/distinfo
470575 biology/clustalx/files
470575 biology/clustalx/files/patch-clustalW_general_VectorOutOfRange.h
470575 biology/clustalx/pkg-descr
biology/clustalx: Multiple alignment of nucleic acid and protein sequences with
GUI

Approved by:    jrm
Differential Revision:  https://reviews.freebsd.org/D15505
Fri, 11 May 2018
[ 00:05 jrm ] Original commit   Revision:469604
469604 biology/Makefile
469604 biology/hyphy
469604 biology/hyphy/Makefile
469604 biology/hyphy/distinfo
469604 biology/hyphy/files
469604 biology/hyphy/files/patch-src_core_calcnode.cpp
469604 biology/hyphy/files/patch-src_core_regex.cpp
469604 biology/hyphy/pkg-descr
469604 biology/hyphy/pkg-plist
New port, biology/hyphy: Hypothesis testing using Phylogenies

WWW: http://www.hyphy.org/
Tue, 24 Apr 2018
[ 14:16 jwb ] Original commit   Revision:468214
468214 biology/Makefile
468214 biology/unanimity
468214 biology/unanimity/Makefile
468214 biology/unanimity/distinfo
468214 biology/unanimity/files
468214 biology/unanimity/files/patch-CMakeLists.txt
468214 biology/unanimity/files/patch-cmake_uny-config.cmake
468214 biology/unanimity/files/patch-cmake_uny-gitsha1.cmake
468214 biology/unanimity/files/patch-include_pacbio_genomicconsensus_Input.h
468214 biology/unanimity/files/patch-include_pacbio_genomicconsensus_Output.h

(Only the first 10 of 13 ports in this commit are shown above. View all ports for this commit)
biology/unanimity: Pacific Biosciences consensus library and applications

Reviewed by:    jrm
Differential Revision:  https://reviews.freebsd.org/D15172
Mon, 23 Apr 2018
[ 16:23 jwb ] Original commit   Revision:468101
468101 biology/Makefile
468101 biology/pbcopper
468101 biology/pbcopper/Makefile
468101 biology/pbcopper/distinfo
468101 biology/pbcopper/files
468101 biology/pbcopper/files/patch-cmake_pbcopper-gitsha1.cmake
468101 biology/pbcopper/pkg-descr
468101 biology/pbcopper/pkg-plist
biology/pbcopper: Core C++ library for Pacific Biosciences tools

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15171
[ 16:08 jwb ] Original commit   Revision:468100
468100 biology/Makefile
468100 biology/pbbam
468100 biology/pbbam/Makefile
468100 biology/pbbam/distinfo
468100 biology/pbbam/pkg-descr
468100 biology/pbbam/pkg-plist
biology/pbbam: PacBio BAM C++ library, with SWIG bindings

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15154
Sat, 21 Apr 2018
[ 17:21 jwb ] Original commit   Revision:467901
467901 biology/Makefile
467901 biology/pbseqan
467901 biology/pbseqan/Makefile
467901 biology/pbseqan/distinfo
467901 biology/pbseqan/pkg-descr
467901 biology/pbseqan/pkg-plist
biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15152
Fri, 20 Apr 2018
[ 01:34 jwb ] Original commit   Revision:467808
467808 biology/Makefile
467808 biology/ddocent
467808 biology/ddocent/Makefile
467808 biology/ddocent/distinfo
467808 biology/ddocent/files
467808 biology/ddocent/files/ddocent-assembly-test
467808 biology/ddocent/files/ddocent-assembly-test-cleanup
467808 biology/ddocent/files/patch-dDocent
467808 biology/ddocent/pkg-descr
467808 biology/ddocent/pkg-plist
biology/ddocent: Bash pipeline for RAD sequencing

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15139
[ 00:07 jwb ] Original commit   Revision:467806
467806 biology/Makefile
467806 biology/freebayes
467806 biology/freebayes/Makefile
467806 biology/freebayes/distinfo
467806 biology/freebayes/files
467806 biology/freebayes/files/patch-Makefile
467806 biology/freebayes/files/patch-SeqLib_bwa_Makefile
467806 biology/freebayes/files/patch-SeqLib_bwa_bwt__lite.c
467806 biology/freebayes/files/patch-SeqLib_bwa_bwtgap.h
467806 biology/freebayes/files/patch-SeqLib_bwa_kthread.c

(Only the first 10 of 16 ports in this commit are shown above. View all ports for this commit)
biology/freebayes: Bayesian haplotype-based polymorphism discovery and
genotyping

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15116
Tue, 17 Apr 2018
[ 03:11 jwb ] Original commit   Revision:467553
467553 biology/Makefile
467553 biology/vcflib
467553 biology/vcflib/Makefile
467553 biology/vcflib/distinfo
467553 biology/vcflib/files
467553 biology/vcflib/files/Makefile.external-libs
467553 biology/vcflib/files/Makefile.submod
467553 biology/vcflib/files/patch-src_cdflib.cpp
467553 biology/vcflib/pkg-descr
467553 biology/vcflib/pkg-plist
biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF files

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15109
Mon, 16 Apr 2018
[ 14:50 jwb ] Original commit   Revision:467485
467485 biology/Makefile
467485 biology/fastahack
467485 biology/fastahack/Makefile
467485 biology/fastahack/distinfo
467485 biology/fastahack/files
467485 biology/fastahack/files/Makefile
467485 biology/fastahack/pkg-descr
467485 biology/fastahack/pkg-plist
biology/fastahack: Utility for indexing and sequence extraction from FASTA files

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15080
Sun, 15 Apr 2018
[ 17:45 jwb ] Original commit   Revision:467402
467402 biology/Makefile
467402 biology/smithwaterman
467402 biology/smithwaterman/Makefile
467402 biology/smithwaterman/distinfo
467402 biology/smithwaterman/files
467402 biology/smithwaterman/files/Makefile
467402 biology/smithwaterman/pkg-descr
467402 biology/smithwaterman/pkg-plist
biology/smithwaterman: Smith-waterman-gotoh alignment algorithm

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15072
Sat, 14 Apr 2018
[ 23:52 jwb ] Original commit   Revision:467343
467343 biology/Makefile
467343 biology/tabixpp
467343 biology/tabixpp/Makefile
467343 biology/tabixpp/distinfo
467343 biology/tabixpp/files
467343 biology/tabixpp/files/Makefile
467343 biology/tabixpp/pkg-descr
biology/tabixpp: C++ wrapper to tabix indexer

Reviewed by:    mat
Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D14977
Wed, 4 Apr 2018
[ 17:21 jwb ] Original commit   Revision:466449
466449 biology/Makefile
466449 biology/pear-merger
466449 biology/pear-merger/Makefile
466449 biology/pear-merger/distinfo
466449 biology/pear-merger/pkg-descr
biology/pear-merger: Memory-efficient and accurate paired-end read merger

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D14959
Tue, 3 Apr 2018
[ 20:57 jwb ] Original commit   Revision:466379
466379 biology/Makefile
466379 biology/seqtk
466379 biology/seqtk/Makefile
466379 biology/seqtk/distinfo
466379 biology/seqtk/files
466379 biology/seqtk/files/patch-Makefile
466379 biology/seqtk/pkg-descr
biology/seqtk: Tool for processing sequences in FASTA/FASTQ format

Approved by:    jrm
Differential Revision:  https://reviews.freebsd.org/D14954
[ 18:23 jwb ] Original commit   Revision:466367
466367 biology/Makefile
466367 biology/trimadap
466367 biology/trimadap/Makefile
466367 biology/trimadap/distinfo
466367 biology/trimadap/files
466367 biology/trimadap/files/patch-Makefile
466367 biology/trimadap/files/patch-kthread.c
466367 biology/trimadap/pkg-descr
biology/trimadap: Trim adapter sequences from Illumina data

Reviewed by:    mat
Approved by:    jrm
Differential Revision:  https://reviews.freebsd.org/D14935
Mon, 2 Apr 2018
[ 16:50 jwb ] Original commit   Revision:466235
466235 biology/Makefile
466235 biology/rainbow
466235 biology/rainbow/Makefile
466235 biology/rainbow/distinfo
466235 biology/rainbow/files
466235 biology/rainbow/files/patch-Makefile
466235 biology/rainbow/pkg-descr
biology/rainbow: Efficient clustering and assembling of short reads

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D14924
Sat, 31 Mar 2018
[ 13:16 jwb ] Original commit   Revision:466048
466048 biology/Makefile
466048 biology/stacks
466048 biology/stacks/Makefile
466048 biology/stacks/distinfo
466048 biology/stacks/files
466048 biology/stacks/files/patch-htslib_Makefile
466048 biology/stacks/pkg-descr
466048 biology/stacks/pkg-message
466048 biology/stacks/pkg-plist
biology/stacks: Software pipeline for building loci from short-read sequences

Reviewed by:    mat
Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D14885
Wed, 28 Mar 2018
[ 13:26 jwb ] Original commit   Revision:465808
465808 biology/Makefile
465808 biology/bamtools
465808 biology/bamtools/Makefile
465808 biology/bamtools/distinfo
465808 biology/bamtools/files
465808 biology/bamtools/files/patch-src_api_internal_io_HostInfo__p.cpp
465808 biology/bamtools/files/patch-src_api_internal_io_TcpSocketEngine__unix__p.cpp
465808 biology/bamtools/pkg-descr
465808 biology/bamtools/pkg-plist
biology/bamtools: API and toolkit for handling BAM files

Approved by:    jrm
Differential Revision:  https://reviews.freebsd.org/D14877
Fri, 22 Dec 2017
[ 01:30 jwb ] Original commit   Revision:456950
456950 biology/Makefile
456950 biology/canu
456950 biology/canu/Makefile
456950 biology/canu/distinfo
456950 biology/canu/files
456950 biology/canu/files/patch-src_pipelines_canu_Execution.pm
456950 biology/canu/pkg-descr
456950 biology/canu/pkg-plist
[new port] biology/canu: Single molecule sequence assembler

Approved by: jrm (mentor) or wen (mentor)
Differential Revision:  https://reviews.freebsd.org/D13574
Sat, 9 Dec 2017
[ 13:23 jwb ] Original commit   Revision:455857
455857 biology/Makefile
455857 biology/p5-TrimGalore
455857 biology/p5-TrimGalore/Makefile
455857 biology/p5-TrimGalore/distinfo
455857 biology/p5-TrimGalore/pkg-descr
455857 biology/p5-TrimGalore/pkg-plist
[new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for adapter
and quality trimming
Approved by: jrm (mentor)
Differential Revision:	D13400
Sat, 2 Dec 2017
[ 20:46 jwb ] Original commit   Revision:455383
455383 biology/Makefile
455383 biology/py-macs2
455383 biology/py-macs2/Makefile
455383 biology/py-macs2/distinfo
455383 biology/py-macs2/pkg-descr
[new port] biology/py-macs2: Analysis of chromatin immunoprecipitation (ChIP)
sequences

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13322
[ 20:44 jwb ] Original commit   Revision:455382
455382 biology/Makefile
455382 biology/kallisto
455382 biology/kallisto/Makefile
455382 biology/kallisto/distinfo
455382 biology/kallisto/files
455382 biology/kallisto/files/kallisto-test.in
455382 biology/kallisto/pkg-descr
[new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq
data

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13328
Thu, 30 Nov 2017
[ 22:54 jwb ] Original commit   Revision:455236
455236 biology/Makefile
455236 biology/fastqc
455236 biology/fastqc/Makefile
455236 biology/fastqc/distinfo
455236 biology/fastqc/pkg-descr
455236 biology/fastqc/pkg-plist
[new port] biology/fastqc: Quality control tool for high throughput sequence
data

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13304
Wed, 29 Nov 2017
[ 22:17 jwb ] Original commit   Revision:455154
455154 biology/Makefile
455154 biology/py-cutadapt
455154 biology/py-cutadapt/Makefile
455154 biology/py-cutadapt/distinfo
455154 biology/py-cutadapt/pkg-descr
455154 biology/py-cutadapt/pkg-plist
[new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, po
ly-A tails, etc
Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13294
Sat, 21 Oct 2017
[ 16:57 jrm ] Original commit   Revision:452595
452595 biology/Makefile
452595 biology/iqtree
452595 biology/iqtree/Makefile
452595 biology/iqtree/distinfo
452595 biology/iqtree/pkg-descr
New port, biology/iqtree: Efficient phylogenomic software

WWW: http://www.iqtree.org/
Fri, 15 Sep 2017
[ 19:17 sunpoet ] Original commit   Revision:449922
449922 biology/Makefile
449922 biology/p5-Bio-FeatureIO
449922 biology/p5-Bio-FeatureIO/Makefile
449922 biology/p5-Bio-FeatureIO/distinfo
449922 biology/p5-Bio-FeatureIO/pkg-descr
449922 biology/p5-Bio-FeatureIO/pkg-plist
Add p5-Bio-FeatureIO 1.6.905

Bio::FeatureIO is an iterator subsystem for genomic sequence features.

Bio::FeatureIO is a handler module for the formats in the FeatureIO set (eg,
Bio::FeatureIO::GFF). It is the officially sanctioned way of getting at the
format objects, which most people should use.

The Bio::FeatureIO system can be thought of like biological file handles. They
are attached to filehandles with smart formatting rules (eg, GFF format, or BED
format) and can either read or write feature objects (Bio::SeqFeature objects,
or more correctly, Bio::FeatureHolderI implementing objects, of which
Bio::SeqFeature is one such object). If you want to know what to do with a
Bio::SeqFeatureI object, read Bio::SeqFeatureI.

The idea is that you request a stream object for a particular format. All the
stream objects have a notion of an internal file that is read from or written
to. A particular FeatureIO object instance is configured for either input or
output. A specific example of a stream object is the Bio::FeatureIO::gff object.

WWW: http://search.cpan.org/dist/Bio-FeatureIO/
Wed, 23 Aug 2017
[ 11:33 rene ] Original commit   Revision:448603
448603 LEGAL
448603 MOVED
448603 audio/Makefile
448603 audio/linux-neroaaccodec
448603 biology/Makefile
448603 biology/biojava
448603 devel/Makefile
448603 devel/gdb66
448603 devel/insight
448603 games/Makefile

(Only the first 10 of 26 ports in this commit are shown above. View all ports for this commit)
Remove expired ports:
2017-08-23 games/plee-the-bear: Broken for more than 6 months
2017-08-23 x11-themes/kde-icons-umicons: Broken for more than 6 months
2017-08-23 lang/bigloo: Broken for more than 6 months
2017-08-23 audio/linux-neroaaccodec: Broken for more than 6 months
2017-08-23 x11-themes/kde-icons-dark-glass: Broken for more than 6 months
2017-08-23 misc/fortune-mod-ferengi_rules_of_acquisition: Broken for more than 6
months
2017-08-23 misc/fortune-mod-culmea-culmilor: Broken for more than 6 months
2017-08-23 misc/xyzcmd: Broken for more than 6 months
2017-08-23 russian/fortuneru: Broken for more than 6 months
2017-08-23 security/bdc: Broken for more than 6 months
2017-08-23 x11-themes/kde-icons-icosx: Broken for more than 6 months
2017-08-23 devel/insight: Broken for more than 6 months
2017-08-23 devel/gdb66: Broken for more than 6 months
2017-08-23 biology/biojava: Broken for more than 6 months
2017-08-23 games/xroach: Broken for more than 6 months
Sat, 6 May 2017
[ 06:07 miwi ] Original commit   Revision:440232
440232 biology/Makefile
440232 biology/py-bx-python
440232 biology/py-bx-python/Makefile
440232 biology/py-bx-python/distinfo
440232 biology/py-bx-python/pkg-descr
bx-python is a python library and associated set of scripts to allow for rapid
implementation of genome scale analyses. The library contains a variety of
useful modules, but the particular strengths are:

Classes for reading and working with genome-scale multiple local alignments
(in MAF, AXT, and LAV formats). Generic data structure for indexing on disk
files that contain blocks of data associated with intervals on various
sequences (used, for example, to provide random access to individual
alignments in huge files; optomized for use over network filesystems).
Data structures for working with intervals on sequences:
 * "Binned bitsets" which act just like chromosome sized bit arrays,
   but lazily allocate regions and allow large blocks of all set or
   all unset bits to be stored compactly
 * "Intersecter" for performing fast intersection tests that preserve
   both query and target intervals and associated annotation

WWW: https://github.com/bxlab/bx-python

PR:		218757
Submitted by:	Yuri Victorovich <yuri@rawbw.com>
[ 06:05 miwi ] Original commit   Revision:440231
440231 biology/Makefile
440231 biology/py-pysam
440231 biology/py-pysam/Makefile
440231 biology/py-pysam/distinfo
440231 biology/py-pysam/files
440231 biology/py-pysam/files/patch-setup.py
440231 biology/py-pysam/pkg-descr
pysam is a lightweight wrapper of the htslib C-API and provides facilities to
read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files as well as access
to the command line functionality of the samtools and bcftools packages. The
module supports compression and random access through indexing.

This module provides a low-level wrapper around the htslib C-API as using
cython and a high-level API for convenient access to the data within standard
genomic file formats.

WWW: https://pypi.python.org/pypi/pysam

PR:		218745
Submitted by:	Yuri Victorovich <yuri@rawbw.com>

Number of commits found XX: 220 (showing only 100 on this page)

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