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Number of commits found: 198 (showing only 100 on this page)

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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>
Sun, 30 Apr 2017
[ 15:47 ler ] Original commit   Revision:439826
439826 MOVED
439826 audio/Makefile
439826 audio/last-cmus
439826 audio/logitechmediaserver-superdatetime
439826 audio/mehdiaplayer
439826 audio/pidgin-musictracker
439826 audio/xpi-musicpm
439826 biology/Makefile
439826 biology/treeviewx
439826 chinese/Makefile

(Only the first 10 of 147 ports in this commit are shown above. View all ports for this commit)
2017-04-30 devel/stormlib-ghost++: Unfetchable for more than six months (google
code has gone away)
2017-04-30 devel/py-coil: Unfetchable for more than six months (google code has
gone away)
2017-04-30 devel/py-cmdln: Unfetchable for more than six months (google code has
gone away)
2017-04-30 devel/privman: Unfetchable for more than six months (google code has
gone away)
2017-04-30 devel/c-unit: Unfetchable for more than six months (google code has
gone away)
2017-04-30 devel/py-px: Unfetchable for more than six months (google code has
gone away)
2017-04-30 devel/nglogc: Unfetchable for more than six months (google code has
gone away)
2017-04-30 devel/bncsutil-ghost++: Unfetchable for more than six months (google
code has gone away)
2017-04-30 devel/liblouisxml: Unfetchable for more than six months (google code
has gone away)
2017-04-30 devel/nxt-python: Unfetchable for more than six months (google code
has gone away)
2017-04-30 devel/spdict: Unfetchable for more than six months (google code has
gone away)
2017-04-30 devel/guiloader-c++: Unfetchable for more than six months (google
code has gone away)
2017-04-30 devel/streamhtmlparser: Unfetchable for more than six months (google
code has gone away)
2017-04-30 devel/winpdb: Unfetchable for more than six months (google code has
gone away)
2017-04-30 net/opendpi: Unfetchable for more than six months (google code has
gone away)
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Sun, 5 Feb 2017
[ 04:26 sunpoet ] Original commit   Revision:433348
433348 MOVED
433348 biology/Makefile
433348 biology/rubygem-bio
433348 biology/rubygem-bio/Makefile
433348 devel/Makefile
433348 devel/rubygem-bio
Move devel/rubygem-bio to biology/rubygem-bio
Mon, 19 Dec 2016
[ 15:54 sunpoet ] Original commit   Revision:428942
428942 biology/Makefile
428942 biology/p5-Bio-Coordinate
428942 biology/p5-Bio-Coordinate/Makefile
428942 biology/p5-Bio-Coordinate/distinfo
428942 biology/p5-Bio-Coordinate/pkg-descr
428942 biology/p5-Bio-Coordinate/pkg-plist
- Add p5-Bio-Coordinate 1.007001

Bio::Coordinate classes are used for working with various biological coordinate
systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples.

WWW: http://search.cpan.org/dist/Bio-Coordinate/
Sun, 18 Dec 2016
[ 15:25 sunpoet ] Original commit   Revision:428872
428872 biology/Makefile
428872 biology/p5-BioPerl-Run
428872 biology/p5-BioPerl-Run/Makefile
428872 biology/p5-bioperl-run
- Move biology/p5-bioperl-run to biology/p5-BioPerl-Run
- Sort *_DEPENDS
- Add NO_ARCH
- Bump PORTREVISION for biology/p5-bioperl renaming
[ 15:25 sunpoet ] Original commit   Revision:428868
428868 biology/Makefile
428868 biology/p5-BioPerl
428868 biology/p5-BioPerl/Makefile
428868 biology/p5-bioperl
- Move biology/p5-bioperl to biology/p5-BioPerl
- Sort *_DEPENDS
- Bump PORTREVISION for dependent ports
Wed, 16 Nov 2016
[ 14:52 jrm ] Original commit   Revision:426241
426241 MOVED
426241 biology/Makefile
426241 biology/njplot
426241 biology/njplot/Makefile
426241 biology/njplot/distinfo
426241 biology/njplot/files/patch-makefile
biology/njplot: Revive and update to version 2.4

Approved by:	AMDmi3 (mentor)
Differential Revision:	https://reviews.freebsd.org/D8518
Mon, 4 Jul 2016
[ 20:48 rene ] Original commit   Revision:418057
418057 LEGAL
418057 MOVED
418057 archivers/Makefile
418057 archivers/epkg
418057 audio/Makefile
418057 audio/alac
418057 audio/hawkvoice
418057 audio/mangler
418057 audio/streamtuner
418057 biology/Makefile

(Only the first 10 of 250 ports in this commit are shown above. View all ports for this commit)
Remove expired ports without open PRs:
2016-07-04 security/openpgpsdk: Broken for more than 6 months
2016-07-04 security/radiusniff: Broken for more than 6 months
2016-07-04 security/pear-Auth_OpenID: Broken for more than 6 months
2016-07-04 security/sshit: Broken for more than 6 months
2016-07-04 security/ifd-slb_rf60: Broken for more than 6 months
2016-07-04 security/rainbowcrack: Broken for more than 6 months
2016-07-04 security/vlog: Broken for more than 6 months
2016-07-04 security/cryptstring: Broken for more than 6 months
2016-07-04 x11/libdnd: Broken for more than 6 months
2016-07-04 x11/xlupe: Broken for more than 6 months
2016-07-04 x11/xco: Broken for more than 6 months
2016-07-04 x11/xclick: Broken for more than 6 months
2016-07-04 devel/ocfpcsc: Broken for more than 6 months
2016-07-04 devel/dits: Broken for more than 6 months
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Tue, 10 May 2016
[ 01:05 junovitch ] Original commit   Revision:414898
414898 UPDATING
414898 biology/Makefile
414898 biology/seqan/Makefile
414898 biology/seqan/distinfo
414898 biology/seqan/files
414898 biology/seqan/pkg-descr
414898 biology/seqan/pkg-plist
414898 biology/seqan1
414898 biology/seqan1/Makefile
414898 biology/seqan1/files

(Only the first 10 of 12 ports in this commit are shown above. View all ports for this commit)
biology/seqan: update 1.3.1 -> 2.1.1
biology/seqan1: create port from current SeqAn 1.3.1 for legacy usage
UPDATING: document SeqAn updates and seqan1 port for legacy usage

PR:		204127
Submitted by:	Hannes Hauswedell <h2+fbsdports@fsfe.org>
[ 00:52 junovitch ] Original commit   Revision:414897
414897 biology/Makefile
414897 biology/seqan-apps
414897 biology/seqan-apps/Makefile
414897 biology/seqan-apps/distinfo
414897 biology/seqan-apps/pkg-descr
414897 biology/seqan-apps/pkg-plist
New port: biology/seqan-apps

SeqAn is an open source C++ library of efficient algorithms
and data structures for the analysis of sequences with the
focus on biological data.

This port contains applications built on SeqAn and developed
within the SeqAn project. Among them are famous read mappers
like RazerS and Yara, as well as many other tools. Some
applications are packaged seperately and the library
can be found at biology/seqan.

WWW: http://www.seqan.de/

PR:		204127
Submitted by:	Hannes Hauswedell <h2+fbsdports@fsfe.org>
Mon, 9 May 2016
[ 16:37 olivierd ] Original commit   Revision:414865
414865 biology/Makefile
414865 biology/py-biom-format
414865 biology/py-biom-format/Makefile
414865 biology/py-biom-format/distinfo
414865 biology/py-biom-format/pkg-descr
The BIOM file format (canonically pronounced biome) is designed to be a
general-use format for representing biological sample by observation contingency
tables. BIOM is a recognized standard for the Earth Microbiome Project and is a
Genomics Standards Consortium supported project.

The BIOM format is designed for general use in broad areas of comparative
-omics. For example, in marker-gene surveys, the primary use of this format is
to represent OTU tables: the observations in this case are OTUs and the matrix
contains counts corresponding to the number of times each OTU is observed in
each sample. With respect to metagenome data, this format would be used to
represent metagenome tables: the observations in this case might correspond to
SEED subsystems, and the matrix would contain counts corresponding to the number
of times each subsystem is observed in each metagenome. Similarly, with respect
to genome data, this format may be used to represent a set of genomes: the
observations in this case again might correspond to SEED subsystems, and the
counts would correspond to the number of times each subsystem is observed in
each genome.

WWW: http://biom-format.org/

PR:		209193
Submitted by:	Joseph Mingrone
Fri, 6 May 2016
[ 08:45 wen ] Original commit   Revision:414686
414686 biology/Makefile
414686 biology/diamond
414686 biology/diamond/Makefile
414686 biology/diamond/distinfo
414686 biology/diamond/files
414686 biology/diamond/files/patch-CMakeLists.txt
414686 biology/diamond/pkg-descr
DNA query sequences against a protein reference database (BLASTP and BLASTX
alignment mode). The speedup over BLAST is up to 20,000 on short reads at a
typical sensitivity of 90-99% relative to BLAST depending on the data and
settings.

WWW: http://ab.inf.uni-tuebingen.de/software/diamond/

PR:		208998
Submitted by:	jrm@ftfl.ca
Thu, 24 Mar 2016
[ 13:53 amdmi3 ] Original commit   Revision:411785
411785 biology/Makefile
411785 biology/jellyfish
411785 biology/jellyfish/Makefile
411785 biology/jellyfish/distinfo
411785 biology/jellyfish/files
411785 biology/jellyfish/files/patch-include_jellyfish_file__header.hpp
411785 biology/jellyfish/pkg-descr
411785 biology/jellyfish/pkg-plist
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
A k-mer is a substring of length k, and counting the occurrences of all such
substrings is a central step in many analyses of DNA sequence. JELLYFISH can
count k-mers quickly by using an efficient encoding of a hash table and by
exploiting the "compare-and-swap" CPU instruction to increase parallelism.

WWW: http://www.genome.umd.edu/jellyfish.html

PR:		207929
Submitted by:	bacon4000@gmail.com
Wed, 23 Mar 2016
[ 11:22 rakuco ] Original commit   Revision:411698
411698 biology/Makefile
411698 biology/bowtie2
411698 biology/bowtie2/Makefile
411698 biology/bowtie2/distinfo
411698 biology/bowtie2/files
411698 biology/bowtie2/files/patch-Makefile
411698 biology/bowtie2/pkg-descr
411698 biology/bowtie2/pkg-plist
New port: biology/bowtie2.

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
reads per hour.

This is Bowtie version 2, which will need to coexists with Bowtie 1 for the
foreseeable future. Both are required by certain genomics pipelines, in some
cases (e.g. Trinity) by the same pipeline.

WWW: https://github.com/BenLangmead/bowtie2

PR:		207908
Submitted by:	Jason Bacon <bacon4000@gmail.com>
[ 11:00 rakuco ] Original commit   Revision:411697
411697 biology/Makefile
411697 biology/slclust
411697 biology/slclust/Makefile
411697 biology/slclust/distinfo
411697 biology/slclust/files
411697 biology/slclust/files/patch-include_cmd__line__opts.h
411697 biology/slclust/files/patch-src_Makefile
411697 biology/slclust/pkg-descr
New port: biology/slclust.

Slclust is a utility that performs single-linkage clustering with the option of
applying a Jaccard similarity coefficient to break weakly bound clusters into
distinct clusters.

WWW: http://sourceforge.net/projects/slclust/

PR:		207997
Submitted by:	Jason Bacon <bacon4000@gmail.com>
Thu, 17 Mar 2016
[ 08:21 wen ] Original commit   Revision:411261
411261 biology/Makefile
411261 biology/trimmomatic
411261 biology/trimmomatic/Makefile
411261 biology/trimmomatic/distinfo
411261 biology/trimmomatic/pkg-descr
411261 biology/trimmomatic/pkg-plist
Trimmomatic performs a variety of useful trimming tasks for illumina
NGS paired-end and single ended data.

WWW: http://www.usadellab.org/cms/?page=trimmomatic

PR:		208044
Submitted by:	bacon4000@gmail.com
Wed, 16 Mar 2016
[ 20:12 pi ] Original commit   Revision:411246
411246 biology/Makefile
411246 biology/p5-transdecoder
411246 biology/p5-transdecoder/Makefile
411246 biology/p5-transdecoder/distinfo
411246 biology/p5-transdecoder/pkg-descr
411246 biology/p5-transdecoder/pkg-plist
New port: biology/p5-transdecoder

TransDecoder identifies candidate coding regions within transcript
sequences, such as those generated by de novo RNA-Seq transcript
assembly using Trinity, or constructed based on RNA-Seq alignments
to the genome using Tophat and Cufflinks.

WWW: http://transdecoder.github.io/

PR:		207993
Submitted by:	Jason Bacon <bacon4000@gmail.com>
Sat, 5 Mar 2016
[ 13:21 rakuco ] Original commit   Revision:410180
410180 biology/Makefile
410180 biology/bowtie
410180 biology/bowtie/Makefile
410180 biology/bowtie/distinfo
410180 biology/bowtie/files
410180 biology/bowtie/files/patch-Makefile
410180 biology/bowtie/pkg-descr
410180 biology/bowtie/pkg-plist
New port: biology/bowtie.

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
reads per hour.

WWW: http://bowtie-bio.sourceforge.net/index.shtml

PR:		206939
Submitted by:	Jason Bacon <bacon4000@gmail.com>
Fri, 26 Feb 2016
[ 17:07 rakuco ] Original commit   Revision:409624
409624 biology/Makefile
409624 biology/vcftools
409624 biology/vcftools/Makefile
409624 biology/vcftools/distinfo
409624 biology/vcftools/pkg-descr
409624 biology/vcftools/pkg-plist
New port: biology/vcftools.

A set of tools written in Perl and C++ for working with VCF files, such as
those generated by the 1000 Genomes Project.

WWW: https://github.com/vcftools/vcftools

PR:		206926
Submitted by:	Jason Bacon <bacon4000@gmail.com>
Tue, 19 Jan 2016
[ 08:56 wen ] Original commit   Revision:406676
406676 biology/Makefile
406676 biology/bedtools
406676 biology/bedtools/Makefile
406676 biology/bedtools/distinfo
406676 biology/bedtools/files
406676 biology/bedtools/files/patch-Makefile
406676 biology/bedtools/pkg-descr
406676 biology/bedtools/pkg-plist
The bedtools utilities are a suite of tools for performing a wide range of
genomics analysis tasks.  The most widely-used of these tools enable genome
arithmetic, i.e., set theory on the genome.  For example, with bedtools one
can intersect, merge, count, complement, and shuffle genomic intervals from
multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.

Although each individual utility is designed to do a relatively simple task,
e.g., intersect two interval files, more sophisticated analyses can be
conducted by stringing together multiple bedtools operations on the command
line or in shell scripts.

WWW: http://bedtools.readthedocs.org/

PR:		204536
Submitted by:	scottcheloha@gmail.com
Sat, 28 Nov 2015
[ 23:08 rene ] Original commit   Revision:402562
402562 MOVED
402562 archivers/Makefile
402562 archivers/wzip
402562 astro/Makefile
402562 astro/aa
402562 astro/dgpsip
402562 astro/ephem
402562 astro/sky2000
402562 astro/wmglobe
402562 audio/Makefile

(Only the first 10 of 114 ports in this commit are shown above. View all ports for this commit)
Remove expired ports:
2015-11-26 audio/pecl-id3: Broken for more than 6 months
2015-11-26 dns/geta: Broken for more than 6 months
2015-11-26 finance/openerp-web: Broken for more than 6 months
2015-11-26 devel/py-async: Further using of this module is not encouraged by
upstream
2015-11-26 chinese/kon2: Depends on expiring chinese/cce
2015-11-26 games/linux-skulltag: Depends on expiring audio/linux-fmodapi
2015-11-26 archivers/wzip: Broken for more than 6 months
2015-11-26 databases/sybtcl: Broken for more than 6 months
2015-11-26 biology/povchem: Broken for more than 6 months
2015-11-26 audio/btc: Broken for more than 6 months
2015-11-26 astro/wmglobe: Broken for more than 6 months
2015-11-26 graphics/pyro: Broken for more than 6 months
2015-11-26 graphics/jpeg2ps: Broken for more than 6 months
2015-11-26 chinese/gugod-clean: Broken for more than 6 months
(Only the first 15 lines of the commit message are shown above View all of this commit message)
Fri, 25 Sep 2015
[ 18:39 rm ] Original commit   Revision:397851
397851 biology/Makefile
397851 biology/bwa
397851 biology/bwa/Makefile
397851 biology/bwa/distinfo
397851 biology/bwa/files
397851 biology/bwa/files/patch-Makefile
397851 biology/bwa/files/patch-bwt_lite.c
397851 biology/bwa/files/patch-bwtgap.c
397851 biology/bwa/files/patch-bwtgap.h
397851 biology/bwa/pkg-descr
BWA is a program for aligning sequencing reads against a large reference
genome (e.g. human genome). It has two major components, one for read shorter
than 150bp and the other for longer reads.

WWW: http://sourceforge.net/projects/bio-bwa/

PR:		203158
Submitted by:	Jason Bacon <jwbacon@tds.net>
[ 18:37 rm ] Original commit   Revision:397850
397850 biology/Makefile
397850 biology/cdbfasta
397850 biology/cdbfasta/Makefile
397850 biology/cdbfasta/distinfo
397850 biology/cdbfasta/files
397850 biology/cdbfasta/files/patch-Makefile
397850 biology/cdbfasta/pkg-descr
Fast indexing and retrieval of FASTA records from flat file data bases.

WWW: http://sourceforge.net/projects/cdbfasta/

PR:		203233
Submitted by:	Jason Bacon <jwbacon@tds.net>

Number of commits found: 198 (showing only 100 on this page)

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