diff options
Diffstat (limited to 'biology')
226 files changed, 226 insertions, 0 deletions
diff --git a/biology/abyss/Makefile b/biology/abyss/Makefile index 20c6e94c67f2..e0ab408418d5 100644 --- a/biology/abyss/Makefile +++ b/biology/abyss/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org COMMENT= Assembly By Short Sequences: parallel, paired-end sequence assembler +WWW= https://www.bcgsc.ca/resources/software/abyss LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/ad2vcf/Makefile b/biology/ad2vcf/Makefile index 42033ae818e0..a07d29427405 100644 --- a/biology/ad2vcf/Makefile +++ b/biology/ad2vcf/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Add allelic depth info from a SAM stream to a VCF file +WWW= https://github.com/auerlab/ad2vcf LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/artemis/Makefile b/biology/artemis/Makefile index 9daae2fc5aa0..484da75e1f9e 100644 --- a/biology/artemis/Makefile +++ b/biology/artemis/Makefile @@ -6,6 +6,7 @@ CATEGORIES= biology java MAINTAINER= yuri@FreeBSD.org COMMENT= DNA sequence viewer and annotation tool +WWW= https://www.sanger.ac.uk/science/tools/artemis LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/avida/Makefile b/biology/avida/Makefile index 255284dc923e..1c44a5fd5b52 100644 --- a/biology/avida/Makefile +++ b/biology/avida/Makefile @@ -6,6 +6,7 @@ MASTER_SITES= SF/${PORTNAME}/${PORTNAME}-stable/${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= Auto-adaptive genetic system designed for ALife research +WWW= https://avida.devosoft.org/ LICENSE= GPLv3 diff --git a/biology/babel/Makefile b/biology/babel/Makefile index 6c128743248f..9c376d8f201b 100644 --- a/biology/babel/Makefile +++ b/biology/babel/Makefile @@ -7,6 +7,7 @@ MASTER_SITES= http://smog.com/chem/babel/files/ \ MAINTAINER= ports@FreeBSD.org COMMENT= Converts among various molecular file formats +WWW= http://smog.com/chem/babel/ CONFLICTS_INSTALL= openbabel diff --git a/biology/bamtools/Makefile b/biology/bamtools/Makefile index 1028dac62f64..03f62b1e6919 100644 --- a/biology/bamtools/Makefile +++ b/biology/bamtools/Makefile @@ -6,6 +6,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= API and toolkit for handling BAM files +WWW= https://github.com/pezmaster31/bamtools LICENSE= MIT diff --git a/biology/bamutil/Makefile b/biology/bamutil/Makefile index 17e8902bc633..485df533807e 100644 --- a/biology/bamutil/Makefile +++ b/biology/bamutil/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Utilities for working with SAM/BAM files +WWW= https://github.com/statgen/bamUtil LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/copyrights/COPYING diff --git a/biology/bbmap/Makefile b/biology/bbmap/Makefile index 9527ee8f4076..2c09e28065fa 100644 --- a/biology/bbmap/Makefile +++ b/biology/bbmap/Makefile @@ -6,6 +6,7 @@ DISTNAME= BBMap_${PORTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= BBMap short read aligner, and other bioinformatic tools +WWW= https://jgi.doe.gov/data-and-tools/bbtools/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt diff --git a/biology/bcftools/Makefile b/biology/bcftools/Makefile index 414f9f5dfa3d..fcea2008869c 100644 --- a/biology/bcftools/Makefile +++ b/biology/bcftools/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Tools for manipulating next-generation sequencing data +WWW= https://www.htslib.org/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/bedtools/Makefile b/biology/bedtools/Makefile index 99de841f40ec..a69f31ec0bbb 100644 --- a/biology/bedtools/Makefile +++ b/biology/bedtools/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Toolset for genome set arithmetic such as intersect, union +WWW= https://bedtools.readthedocs.org/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/bfc/Makefile b/biology/bfc/Makefile index 967e8829f16a..30f810f8b92c 100644 --- a/biology/bfc/Makefile +++ b/biology/bfc/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Correct sequencing errors from Illumina sequencing data +WWW= https://github.com/lh3/bfc LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE.txt diff --git a/biology/bio-mocha/Makefile b/biology/bio-mocha/Makefile index 97a2753ddad9..fb552c0676e7 100644 --- a/biology/bio-mocha/Makefile +++ b/biology/bio-mocha/Makefile @@ -7,6 +7,7 @@ DISTFILES+= ${PORTNAME}_${DISTVERSION}-20220112.tar.gz MAINTAINER= jwb@FreeBSD.org COMMENT= Bcftools plugin for mosaic chromosomal alteration analysis +WWW= https://software.broadinstitute.org/software/mocha/ LICENSE= MIT diff --git a/biology/bioawk/Makefile b/biology/bioawk/Makefile index d4ee881f6bb4..c5bccd238213 100644 --- a/biology/bioawk/Makefile +++ b/biology/bioawk/Makefile @@ -6,6 +6,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= BWK awk modified for biological data +WWW= https://github.com/lh3/bioawk LICENSE= BSD3CLAUSE diff --git a/biology/biococoa/Makefile b/biology/biococoa/Makefile index fe557b9bc3a8..17daabfa30ab 100644 --- a/biology/biococoa/Makefile +++ b/biology/biococoa/Makefile @@ -8,6 +8,7 @@ EXTRACT_SUFX= .tgz MAINTAINER= ports@FreeBSD.org COMMENT= Bioinformatics framework +WWW= http://bioinformatics.org/biococoa/ LICENSE= LGPL21 diff --git a/biology/biolibc-tools/Makefile b/biology/biolibc-tools/Makefile index b13902d38c82..d61b832c18c2 100644 --- a/biology/biolibc-tools/Makefile +++ b/biology/biolibc-tools/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= High-performance bioinformatics tools based on biolibc +WWW= https://github.com/auerlab/biolibc-tools LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/biolibc/Makefile b/biology/biolibc/Makefile index f828f7e98752..7867ba897c47 100644 --- a/biology/biolibc/Makefile +++ b/biology/biolibc/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Low-level high-performance bioinformatics library +WWW= https://github.com/auerlab/biolibc LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/bioparser/Makefile b/biology/bioparser/Makefile index 2f83de5c9873..3733b9b8ea29 100644 --- a/biology/bioparser/Makefile +++ b/biology/bioparser/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology devel MAINTAINER= yuri@FreeBSD.org COMMENT= C++ header-only parsing library for several formats in bioinformatics +WWW= https://github.com/rvaser/bioparser LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/biosig/Makefile b/biology/biosig/Makefile index 6dd6c6b3c1eb..274cc42f6240 100644 --- a/biology/biosig/Makefile +++ b/biology/biosig/Makefile @@ -6,6 +6,7 @@ DISTNAME= ${PORTNAME}-${PORTVERSION}.src MAINTAINER= yuri@FreeBSD.org COMMENT= Library for reading and writing different biosignal data format +WWW= http://biosig.sourceforge.net/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING diff --git a/biology/biosoup/Makefile b/biology/biosoup/Makefile index f4e9db28e57e..56ab6b148060 100644 --- a/biology/biosoup/Makefile +++ b/biology/biosoup/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology devel MAINTAINER= yuri@FreeBSD.org COMMENT= Collection of C++ header-only data structures for bioinformatics +WWW= https://github.com/rvaser/biosoup LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/biostar-tools/Makefile b/biology/biostar-tools/Makefile index 8e23e40fd1b7..faa45754c02c 100644 --- a/biology/biostar-tools/Makefile +++ b/biology/biostar-tools/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology python MAINTAINER= jwb@FreeBSD.org COMMENT= Meta-port for Biostar Handbook tools +WWW= https://www.biostarhandbook.com LICENSE= BSD2CLAUSE diff --git a/biology/bolt-lmm/Makefile b/biology/bolt-lmm/Makefile index 8c9115ce7c0f..f1e10878d6a3 100644 --- a/biology/bolt-lmm/Makefile +++ b/biology/bolt-lmm/Makefile @@ -7,6 +7,7 @@ DISTNAME= BOLT-LMM_v${PORTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= Mixed model association testing and variance component analysis +WWW= https://data.broadinstitute.org/alkesgroup/BOLT-LMM/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/license.txt diff --git a/biology/bowtie/Makefile b/biology/bowtie/Makefile index 575c1264b7b6..e2492fd25213 100644 --- a/biology/bowtie/Makefile +++ b/biology/bowtie/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Ultrafast, memory-efficient short read aligner +WWW= http://bowtie-bio.sourceforge.net/index.shtml LICENSE= ART10 diff --git a/biology/bowtie2/Makefile b/biology/bowtie2/Makefile index 675ce768cebc..6ca11a69916f 100644 --- a/biology/bowtie2/Makefile +++ b/biology/bowtie2/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology perl5 python MAINTAINER= jwb@FreeBSD.org COMMENT= Ultrafast, memory-efficient short read aligner +WWW= https://github.com/BenLangmead/bowtie2 LICENSE= GPLv3+ LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/bwa/Makefile b/biology/bwa/Makefile index d98fad06941f..2a00dfef9b44 100644 --- a/biology/bwa/Makefile +++ b/biology/bwa/Makefile @@ -9,6 +9,7 @@ PATCHFILES= 2a1ae7b6f34a96ea25be007ac9d91e57e9d32284.patch:-p1 MAINTAINER= jwb@FreeBSD.org COMMENT= Burrows-Wheeler sequence aligner +WWW= https://sourceforge.net/projects/bio-bwa/ LICENSE= GPLv3 diff --git a/biology/canu/Makefile b/biology/canu/Makefile index 3e06832ca772..c549003dea6f 100644 --- a/biology/canu/Makefile +++ b/biology/canu/Makefile @@ -7,6 +7,7 @@ MASTER_SITES= https://github.com/marbl/canu/releases/download/v${DISTVERSION}/ MAINTAINER= jwb@FreeBSD.org COMMENT= Single molecule sequence assembler +WWW= https://canu.readthedocs.io/ LICENSE= GPLv2 LICENSE_FILE= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/README.license.GPL diff --git a/biology/cd-hit/Makefile b/biology/cd-hit/Makefile index c93119761311..4c27a9175716 100644 --- a/biology/cd-hit/Makefile +++ b/biology/cd-hit/Makefile @@ -6,6 +6,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Clustering and comparing protein or nucleotide sequences +WWW= http://weizhong-lab.ucsd.edu/cd-hit/ LICENSE= GPLv2 diff --git a/biology/cdbfasta/Makefile b/biology/cdbfasta/Makefile index 908b4b59143c..8a30ab65ee8d 100644 --- a/biology/cdbfasta/Makefile +++ b/biology/cdbfasta/Makefile @@ -5,6 +5,7 @@ MASTER_SITES= http://acadix.biz/Ports/distfiles/ MAINTAINER= jwb@FreeBSD.org COMMENT= Fast indexing and retrieval of FASTA records from flat file databases +WWW= https://sourceforge.net/projects/cdbfasta/ # LICENSE= unspecified diff --git a/biology/checkm/Makefile b/biology/checkm/Makefile index 6b9377adbf8b..e0e287e0e668 100644 --- a/biology/checkm/Makefile +++ b/biology/checkm/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology python MAINTAINER= yuri@FreeBSD.org COMMENT= Quality assessment tool for the microbial genomes +WWW= https://ecogenomics.github.io/CheckM/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/clustal-omega/Makefile b/biology/clustal-omega/Makefile index afc129878f68..52e65cb1c170 100644 --- a/biology/clustal-omega/Makefile +++ b/biology/clustal-omega/Makefile @@ -5,6 +5,7 @@ MASTER_SITES= http://www.clustal.org/omega/ MAINTAINER= jwb@FreeBSD.org COMMENT= Multiple alignment of nucleic acid and protein, replaces clustalw +WWW= http://www.clustal.org/omega/ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/COPYING diff --git a/biology/clustalw/Makefile b/biology/clustalw/Makefile index 481261598d01..ae3e9c26aeca 100644 --- a/biology/clustalw/Makefile +++ b/biology/clustalw/Makefile @@ -7,6 +7,7 @@ MASTER_SITES= ftp://ftp.ebi.ac.uk/pub/software/clustalw2/${PORTVERSION}/ \ MAINTAINER= jwb@FreeBSD.org COMMENT= Multiple alignment program for DNA or proteins +WWW= http://www.clustal.org/ LICENSE= LGPL3 LICENSE_FILE= ${WRKSRC}/COPYING diff --git a/biology/cufflinks/Makefile b/biology/cufflinks/Makefile index f05414a5cc75..a9e50241f2ab 100644 --- a/biology/cufflinks/Makefile +++ b/biology/cufflinks/Makefile @@ -10,6 +10,7 @@ PATCHFILES+= ea4671149f3054c773d99cea521db75bf7b0658f.patch:-p1 # https://github MAINTAINER= yuri@FreeBSD.org COMMENT= Cufflinks assembles transcripts, estimates their abundance, etc +WWW= https://cole-trapnell-lab.github.io/cufflinks/ LICENSE= BSL LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/cytoscape/Makefile b/biology/cytoscape/Makefile index ff126eccfa48..1145e1357908 100644 --- a/biology/cytoscape/Makefile +++ b/biology/cytoscape/Makefile @@ -7,6 +7,7 @@ DISTFILES= FreeBSD-${PORTNAME}-${PORTVERSION}-maven-repository.tar.gz:maven MAINTAINER= yuri@FreeBSD.org COMMENT= Software to visualize molecular interaction networks, gene expression +WWW= https://www.cytoscape.org LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/api/LICENSE diff --git a/biology/ddocent/Makefile b/biology/ddocent/Makefile index 52f2eda96af0..e82fd5828e01 100644 --- a/biology/ddocent/Makefile +++ b/biology/ddocent/Makefile @@ -6,6 +6,7 @@ CATEGORIES= biology java perl5 python MAINTAINER= jwb@FreeBSD.org COMMENT= Bash pipeline for RAD sequencing +WWW= http://ddocent.com LICENSE= MIT diff --git a/biology/diamond/Makefile b/biology/diamond/Makefile index 9171c97815a0..a0eaffb8b18b 100644 --- a/biology/diamond/Makefile +++ b/biology/diamond/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org COMMENT= BLAST-compatible local sequence aligner +WWW= http://ab.inf.uni-tuebingen.de/software/diamond/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/dsr-pdb/Makefile b/biology/dsr-pdb/Makefile index 56d1b24bc3f1..ab9e4674bb14 100644 --- a/biology/dsr-pdb/Makefile +++ b/biology/dsr-pdb/Makefile @@ -8,6 +8,7 @@ DIST_SUBDIR= ${PORTNAME}-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Simple C++ PDB reader (reads the protein description format) +WWW= https://graphics.stanford.edu/~drussel/pdb/ LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/COPYING.txt diff --git a/biology/edlib/Makefile b/biology/edlib/Makefile index a9e942ed7bb0..3ec16d24a49b 100644 --- a/biology/edlib/Makefile +++ b/biology/edlib/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org COMMENT= Fast C++ library for sequence alignment using edit distance +WWW= https://github.com/Martinsos/edlib LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/emboss/Makefile b/biology/emboss/Makefile index ec16fe05eba8..d96f7c223ec4 100644 --- a/biology/emboss/Makefile +++ b/biology/emboss/Makefile @@ -8,6 +8,7 @@ DIST_SUBDIR= ${PORTNAME} MAINTAINER= wen@FreeBSD.org COMMENT= Collection of open source tools for genetic sequence analysis +WWW= http://www.emboss.org/ LICENSE= GPLv2 diff --git a/biology/erminej/Makefile b/biology/erminej/Makefile index 39c19e7d2a25..69b22e7884fb 100644 --- a/biology/erminej/Makefile +++ b/biology/erminej/Makefile @@ -6,6 +6,7 @@ DISTNAME= ermineJ-${DISTVERSION}-generic-bundle MAINTAINER= jwb@FreeBSD.org COMMENT= Analyses of gene sets such as gene expression profiling studies +WWW= https://erminej.msl.ubc.ca/ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE.txt diff --git a/biology/exonerate/Makefile b/biology/exonerate/Makefile index f1ffb94e13b0..e194db681c3e 100644 --- a/biology/exonerate/Makefile +++ b/biology/exonerate/Makefile @@ -5,6 +5,7 @@ MASTER_SITES= http://ftp.ebi.ac.uk/pub/software/vertebrategenomics/exonerate/ MAINTAINER= mzaki@niid.go.jp COMMENT= Generic tool for sequence alignment +WWW= https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING diff --git a/biology/fasta/Makefile b/biology/fasta/Makefile index 6b087427a780..ac1e45d9f75d 100644 --- a/biology/fasta/Makefile +++ b/biology/fasta/Makefile @@ -7,6 +7,7 @@ EXTRACT_SUFX= .shar.Z MAINTAINER= ports@FreeBSD.org COMMENT= Collection of programs for searching DNA and protein databases +WWW= http://fasta.bioch.virginia.edu/ # Converted from NO_CDROM LICENSE= FASTA diff --git a/biology/fasta3/Makefile b/biology/fasta3/Makefile index 6a42e93b50ba..7a1fb266f1f4 100644 --- a/biology/fasta3/Makefile +++ b/biology/fasta3/Makefile @@ -7,6 +7,7 @@ DIST_SUBDIR= fasta3/2014-01-29 MAINTAINER= wendell@bsd.com.br COMMENT= Collection of programs for searching DNA and protein databases +WWW= http://fasta.bioch.virginia.edu/ LICENSE= Fasta LICENSE_NAME= Fasta program copyright W. Pearson and U.Virginia diff --git a/biology/fastahack/Makefile b/biology/fastahack/Makefile index ef572419c199..6158082d20b7 100644 --- a/biology/fastahack/Makefile +++ b/biology/fastahack/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Utility for indexing and sequence extraction from FASTA files +WWW= https://github.com/ekg/fastahack LICENSE= GPLv2 diff --git a/biology/fastdnaml/Makefile b/biology/fastdnaml/Makefile index 53c0e16a5003..43010d771944 100644 --- a/biology/fastdnaml/Makefile +++ b/biology/fastdnaml/Makefile @@ -7,6 +7,7 @@ DISTNAME= fastDNAml_${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= Faster DNAML, makes phylogenetic trees using maximum likelihood +WWW= https://www.life.illinois.edu/gary/programs/fastDNAml.html LICENSE= GPLv2+ diff --git a/biology/fastool/Makefile b/biology/fastool/Makefile index a7f6de647809..8248abeaeb7d 100644 --- a/biology/fastool/Makefile +++ b/biology/fastool/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Simple and quick FastQ and FastA tool for file reading and conversion +WWW= https://github.com/fstrozzi/Fastool LICENSE= BSD2CLAUSE diff --git a/biology/fastp/Makefile b/biology/fastp/Makefile index 5f43ff6a80df..a946098298a8 100644 --- a/biology/fastp/Makefile +++ b/biology/fastp/Makefile @@ -6,6 +6,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Ultra-fast all-in-one FASTQ preprocessor +WWW= https://github.com/OpenGene/fastp LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/fastq-trim/Makefile b/biology/fastq-trim/Makefile index 24edd6e89564..d183a3c838ba 100644 --- a/biology/fastq-trim/Makefile +++ b/biology/fastq-trim/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Lightening fast sequence read trimmer +WWW= https://github.com/outpaddling/Fastq-trim LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/fastqc/Makefile b/biology/fastqc/Makefile index b71a1a9778c6..a6ffbc2eaf07 100644 --- a/biology/fastqc/Makefile +++ b/biology/fastqc/Makefile @@ -6,6 +6,7 @@ DISTNAME= ${PORTNAME}_v${DISTVERSIONPREFIX}${DISTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= Quality control tool for high throughput sequence data +WWW= https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE.txt diff --git a/biology/fasttree/Makefile b/biology/fasttree/Makefile index c47e9dabb557..560274658cd1 100644 --- a/biology/fasttree/Makefile +++ b/biology/fasttree/Makefile @@ -7,6 +7,7 @@ EXTRACT_SUFX= .c MAINTAINER= jwb@FreeBSD.org COMMENT= Approximately-maximum-likelihood phylogenetic trees from alignments +WWW= http://www.microbesonline.org/fasttree/ LICENSE= GPLv2+ diff --git a/biology/fastx-toolkit/Makefile b/biology/fastx-toolkit/Makefile index 5e7f8067f298..186707811d00 100644 --- a/biology/fastx-toolkit/Makefile +++ b/biology/fastx-toolkit/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= CLI tools for Short-Reads FASTA/FASTQ files preprocessing +WWW= http://hannonlab.cshl.edu/fastx_toolkit/ LICENSE= AGPLv3+ LICENSE_FILE= ${WRKSRC}/COPYING diff --git a/biology/figtree/Makefile b/biology/figtree/Makefile index f2bb01c8053b..9dd72f07d044 100644 --- a/biology/figtree/Makefile +++ b/biology/figtree/Makefile @@ -6,6 +6,7 @@ CATEGORIES= biology education java MAINTAINER= yuri@FreeBSD.org COMMENT= Graphical viewer of phylogenetic trees +WWW= http://tree.bio.ed.ac.uk/software/figtree/ LICENSE= GPLv2 diff --git a/biology/flash/Makefile b/biology/flash/Makefile index 82af7793197b..7c33bb9ba325 100644 --- a/biology/flash/Makefile +++ b/biology/flash/Makefile @@ -6,6 +6,7 @@ DISTNAME= FLASH-${DISTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= Fast Length Adjustment of SHort reads +WWW= https://ccb.jhu.edu/software/FLASH/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING diff --git a/biology/fluctuate/Makefile b/biology/fluctuate/Makefile index e5b41709b74c..3cd3e1e62966 100644 --- a/biology/fluctuate/Makefile +++ b/biology/fluctuate/Makefile @@ -6,6 +6,7 @@ DISTNAME= ${PORTNAME}1.4.src.doc MAINTAINER= ports@FreeBSD.org COMMENT= Program to fit population models +WWW= https://evolution.genetics.washington.edu/lamarc/fluctuate.html WRKSRC= ${WRKDIR}/${PORTNAME}1.4 ALL_TARGET= ${PORTNAME} diff --git a/biology/freebayes/Makefile b/biology/freebayes/Makefile index a30487d291b1..58324443247a 100644 --- a/biology/freebayes/Makefile +++ b/biology/freebayes/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Bayesian haplotype-based polymorphism discovery and genotyping +WWW= https://github.com/ekg/freebayes LICENSE= MIT diff --git a/biology/garlic/Makefile b/biology/garlic/Makefile index 5872e8a656db..e36058e1a4fa 100644 --- a/biology/garlic/Makefile +++ b/biology/garlic/Makefile @@ -8,6 +8,7 @@ EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} MAINTAINER= ports@FreeBSD.org COMMENT= Molecular viewer, editor, and visualization program +WWW= http://www.zucic.org/garlic/ USES= gmake xorg USE_XORG= x11 diff --git a/biology/gatk/Makefile b/biology/gatk/Makefile index 431ef692bf43..1777820c1440 100644 --- a/biology/gatk/Makefile +++ b/biology/gatk/Makefile @@ -6,6 +6,7 @@ EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} MAINTAINER= yuri@FreeBSD.org COMMENT= Variant discovery in high-throughput sequencing data +WWW= https://gatk.broadinstitute.org/hc/en-us LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.TXT diff --git a/biology/gcta/Makefile b/biology/gcta/Makefile index 37f0edc6cc84..f4a82826d85c 100644 --- a/biology/gcta/Makefile +++ b/biology/gcta/Makefile @@ -9,6 +9,7 @@ DISTFILES= ${PORTNAME}_${DISTVERSION}_src${EXTRACT_SUFX}:main \ MAINTAINER= jwb@FreeBSD.org COMMENT= Genome-wide Complex Trait Analysis +WWW= https://cnsgenomics.com/software/gcta/index.html LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/GNU_General_Public_License_v3.txt diff --git a/biology/gemma/Makefile b/biology/gemma/Makefile index 221f295bf30f..86abc7fc04f1 100644 --- a/biology/gemma/Makefile +++ b/biology/gemma/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Genome-wide Efficient Mixed Model Association +WWW= https://github.com/genetics-statistics/GEMMA LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/generand/Makefile b/biology/generand/Makefile index dc843a03fbc0..2309b97000fc 100644 --- a/biology/generand/Makefile +++ b/biology/generand/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Generate random genomic data in FASTA/FASTQ, SAM, or VCF format +WWW= https://github.com/auerlab/generand LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/gff2ps/Makefile b/biology/gff2ps/Makefile index 01dc7fd70784..cbfe371970df 100644 --- a/biology/gff2ps/Makefile +++ b/biology/gff2ps/Makefile @@ -7,6 +7,7 @@ DISTFILES= ${PORTNAME}_v${PORTVERSION}.gz MAINTAINER= egypcio@FreeBSD.org COMMENT= Convert gff-formatted genomic data sets to PostScript +WWW= https://genome.crg.es/software/gfftools/GFF2PS.html LICENSE= GPLv2+ diff --git a/biology/gffread/Makefile b/biology/gffread/Makefile index c4d6cc13f33e..4f9fb8666803 100644 --- a/biology/gffread/Makefile +++ b/biology/gffread/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= GFF/GTF format conversions, filtering, FASTA extraction, etc +WWW= http://ccb.jhu.edu/software/stringtie/gff.shtml #gffread LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/gmap/Makefile b/biology/gmap/Makefile index 2477d456c629..acde8f9f3f1c 100644 --- a/biology/gmap/Makefile +++ b/biology/gmap/Makefile @@ -6,6 +6,7 @@ DISTNAME= ${PORTNAME}-gsnap-${PORTVERSION:C|\.|-|g} MAINTAINER= jwb@FreeBSD.org COMMENT= Genomic Mapping and Alignment Program for mRNA and EST Sequences +WWW= http://www.gene.com/share/gmap LICENSE= GMAP LICENSE_NAME= GMAP License diff --git a/biology/gperiodic/Makefile b/biology/gperiodic/Makefile index e1d889356b42..46e79e13148b 100644 --- a/biology/gperiodic/Makefile +++ b/biology/gperiodic/Makefile @@ -5,6 +5,7 @@ MASTER_SITES= SF/${PORTNAME} MAINTAINER= ports@FreeBSD.org COMMENT= Displays a periodic table of the elements +WWW= https://sourceforge.net/projects/gperiodic/ LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/gpl.txt diff --git a/biology/graphlan/Makefile b/biology/graphlan/Makefile index 3ff4720566ab..2b25b1d1f996 100644 --- a/biology/graphlan/Makefile +++ b/biology/graphlan/Makefile @@ -11,6 +11,7 @@ DISTFILES= ${PORTNAME}-v${DISTVERSION}-${BB_COMMIT}${EXTRACT_SUFX} \ MAINTAINER= yuri@FreeBSD.org COMMENT= High-quality circular representations of taxonomic, phylogenetic trees +WWW= https://bitbucket.org/nsegata/graphlan/wiki/Home LICENSE= MIT LICENSE_FILE= ${WRKSRC}/license.txt diff --git a/biology/groopm/Makefile b/biology/groopm/Makefile index 9a9b4ce69b9b..f5b0bf7559c4 100644 --- a/biology/groopm/Makefile +++ b/biology/groopm/Makefile @@ -6,6 +6,7 @@ MASTER_SITES= CHEESESHOP MAINTAINER= yuri@FreeBSD.org COMMENT= Metagenomic binning suite +WWW= https://ecogenomics.github.io/GroopM/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE.txt diff --git a/biology/haplohseq/Makefile b/biology/haplohseq/Makefile index 24457a0a6147..c898de46c29c 100644 --- a/biology/haplohseq/Makefile +++ b/biology/haplohseq/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Identify regions of allelic imbalance +WWW= https://sites.google.com/site/integrativecancergenomics/software/haplohseq LICENSE= MIT diff --git a/biology/hhsuite/Makefile b/biology/hhsuite/Makefile index 0c655ea1561a..60e0fcb6ad66 100644 --- a/biology/hhsuite/Makefile +++ b/biology/hhsuite/Makefile @@ -6,6 +6,7 @@ CATEGORIES= biology science MAINTAINER= yuri@FreeBSD.org COMMENT= Remote protein homology detection suite +WWW= https://github.com/soedinglab/hh-suite LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/hisat2/Makefile b/biology/hisat2/Makefile index 8b49bfc49f26..da8449466d81 100644 --- a/biology/hisat2/Makefile +++ b/biology/hisat2/Makefile @@ -6,6 +6,7 @@ CATEGORIES= biology perl5 python MAINTAINER= jwb@FreeBSD.org COMMENT= Alignment program for mapping next-generation sequencing reads +WWW= https://ccb.jhu.edu/software/hisat2/index.shtml LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/hmmer/Makefile b/biology/hmmer/Makefile index ae5bb70e0c2e..3773440431c7 100644 --- a/biology/hmmer/Makefile +++ b/biology/hmmer/Makefile @@ -5,6 +5,7 @@ MASTER_SITES= http://eddylab.org/software/hmmer/ MAINTAINER= mzaki@e-mail.ne.jp COMMENT= Profile hidden Markov models for biological sequence analysis +WWW= http://hmmer.org/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/htslib/Makefile b/biology/htslib/Makefile index ef7c203ad44f..e6daa6552449 100644 --- a/biology/htslib/Makefile +++ b/biology/htslib/Makefile @@ -6,6 +6,7 @@ MASTER_SITES= https://github.com/samtools/htslib/releases/download/${DISTVERSION MAINTAINER= jwb@FreeBSD.org COMMENT= C library for high-throughput sequencing data formats +WWW= https://www.htslib.org/ LICENSE= BSD3CLAUSE MIT LICENSE_COMB= multi diff --git a/biology/hyphy/Makefile b/biology/hyphy/Makefile index dea81b737efd..aeaa0f7c0676 100644 --- a/biology/hyphy/Makefile +++ b/biology/hyphy/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org COMMENT= Hypothesis testing using Phylogenies +WWW= https://www.hyphy.org/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/igv/Makefile b/biology/igv/Makefile index 2b23dc18806e..4018c31c67b5 100644 --- a/biology/igv/Makefile +++ b/biology/igv/Makefile @@ -9,6 +9,7 @@ EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} MAINTAINER= yuri@FreeBSD.org COMMENT= Visualization tool for genomic datasets +WWW= https://software.broadinstitute.org/software/igv/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/license.txt diff --git a/biology/infernal/Makefile b/biology/infernal/Makefile index 5c1717abd965..528494dbb63a 100644 --- a/biology/infernal/Makefile +++ b/biology/infernal/Makefile @@ -5,6 +5,7 @@ MASTER_SITES= http://eddylab.org/infernal/ MAINTAINER= mzaki@e-mail.ne.jp COMMENT= Search sequence databases for structural RNA homologs +WWW= http://eddylab.org/infernal/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/iolib/Makefile b/biology/iolib/Makefile index dd00cda53347..01c667b87882 100644 --- a/biology/iolib/Makefile +++ b/biology/iolib/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= ports@FreeBSD.org COMMENT= General purpose trace file (and Experiment File) reading interface +WWW= http://staden.sourceforge.net/ LICENSE= BSD3CLAUSE diff --git a/biology/iqtree/Makefile b/biology/iqtree/Makefile index 2a9a8b85ce11..e8bd283e0e42 100644 --- a/biology/iqtree/Makefile +++ b/biology/iqtree/Makefile @@ -6,6 +6,7 @@ CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org COMMENT= Efficient phylogenomic software by maximum likelihood +WWW= http://www.iqtree.org/ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/jalview/Makefile b/biology/jalview/Makefile index 8ac9d0712d15..bbdbb954e59d 100644 --- a/biology/jalview/Makefile +++ b/biology/jalview/Makefile @@ -8,6 +8,7 @@ EXTRACT_ONLY= ${DISTNAME}${EXTRACT_SUFX} MAINTAINER= yuri@FreeBSD.org COMMENT= Viewer and editor for multiple sequence alignments +WWW= https://www.jalview.org LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/jellyfish/Makefile b/biology/jellyfish/Makefile index 1a8034e67d4c..d41e1ec1cd42 100644 --- a/biology/jellyfish/Makefile +++ b/biology/jellyfish/Makefile @@ -8,6 +8,7 @@ DISTNAME= ${PORTNAME:tl}-${DISTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= Fast, memory-efficient counting of k-mers in DNA +WWW= http://www.genome.umd.edu/jellyfish.html LICENSE= BSD3CLAUSE GPLv3+ LICENSE_COMB= dual diff --git a/biology/kallisto/Makefile b/biology/kallisto/Makefile index 7b9a563fbef2..d7b66a14f1b7 100644 --- a/biology/kallisto/Makefile +++ b/biology/kallisto/Makefile @@ -7,6 +7,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Quantify abundances of transcripts from RNA-Seq data +WWW= https://pachterlab.github.io/kallisto/about.html LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/license.txt diff --git a/biology/kmcp/Makefile b/biology/kmcp/Makefile index 1e9b7e83f3d2..8ccd55532afa 100644 --- a/biology/kmcp/Makefile +++ b/biology/kmcp/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org COMMENT= Accurate metagenomic profiling & fast large-scale genome searching +WWW= https://bioinf.shenwei.me/kmcp/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/lamarc/Makefile b/biology/lamarc/Makefile index eb9fc5f16e40..9e2de8eaef76 100644 --- a/biology/lamarc/Makefile +++ b/biology/lamarc/Makefile @@ -8,6 +8,7 @@ MASTER_SITES= http://evolution.genetics.washington.edu/lamarc/download/ MAINTAINER= ports@FreeBSD.org COMMENT= Package of programs for computing population parameters +WWW= https://evolution.genetics.washington.edu/lamarc/ LICENSE= APACHE20 diff --git a/biology/libbigwig/Makefile b/biology/libbigwig/Makefile index 62239103ff1e..31ad9b4e2df8 100644 --- a/biology/libbigwig/Makefile +++ b/biology/libbigwig/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org COMMENT= C library for handling bigWig files (containing genomic data) +WWW= https://github.com/dpryan79/libBigWig LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/libgff/Makefile b/biology/libgff/Makefile index 6a16d0cd4557..7fa18c100fe4 100644 --- a/biology/libgff/Makefile +++ b/biology/libgff/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= GFF/GTF parsing library based on GCLib +WWW= https://github.com/COMBINE-lab/libgff LICENSE= BSL LICENSE_FILE= ${WRKSRC}/BoostLicense.txt diff --git a/biology/libgtextutils/Makefile b/biology/libgtextutils/Makefile index 6de2b7cf460e..2911dd8858a0 100644 --- a/biology/libgtextutils/Makefile +++ b/biology/libgtextutils/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Gordon's text utilities +WWW= https://github.com/agordon/libgtextutils LICENSE= AGPLv3 diff --git a/biology/libneurosim/Makefile b/biology/libneurosim/Makefile index 9cdeb48e806b..a833782c9f82 100644 --- a/biology/libneurosim/Makefile +++ b/biology/libneurosim/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org COMMENT= Common interfaces for neuronal simulators +WWW= https://github.com/INCF/libneurosim LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING diff --git a/biology/libnuml/Makefile b/biology/libnuml/Makefile index c7ad5ce86abf..67dd0f9f954d 100644 --- a/biology/libnuml/Makefile +++ b/biology/libnuml/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology devel MAINTAINER= yuri@FreeBSD.org COMMENT= C++ library for Numerical Markup Language +WWW= https://github.com/NuML/NuML LICENSE= LGPL21 diff --git a/biology/libsbml/Makefile b/biology/libsbml/Makefile index f5d022a663e7..dd2265f773ef 100644 --- a/biology/libsbml/Makefile +++ b/biology/libsbml/Makefile @@ -7,6 +7,7 @@ DISTNAME= libSBML-${PORTVERSION}-core-src MAINTAINER= sunpoet@FreeBSD.org COMMENT= API Library for Working with SBML File +WWW= https://sbml.org/software/libsbml/ LICENSE= LGPL21 LICENSE_FILE= ${WRKSRC}/COPYING.txt diff --git a/biology/libsedml/Makefile b/biology/libsedml/Makefile index eea82d1132df..c979cd8bc72f 100644 --- a/biology/libsedml/Makefile +++ b/biology/libsedml/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology devel MAINTAINER= yuri@FreeBSD.org COMMENT= C++ SED-ML library +WWW= https://github.com/fbergmann/libSEDML LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt diff --git a/biology/linux-foldingathome/Makefile b/biology/linux-foldingathome/Makefile index a2f3c6a6dc17..5118ba878abb 100644 --- a/biology/linux-foldingathome/Makefile +++ b/biology/linux-foldingathome/Makefile @@ -8,6 +8,7 @@ EXTRACT_SUFX= .x86_64.rpm MAINTAINER= 0mp@FreeBSD.org COMMENT= Folding@home Client +WWW= https://foldingathome.org/ # Distribution without permission is prohibited LICENSE= FAHSL diff --git a/biology/mafft/Makefile b/biology/mafft/Makefile index f273c63c0488..61f225828684 100644 --- a/biology/mafft/Makefile +++ b/biology/mafft/Makefile @@ -6,6 +6,7 @@ DISTNAME= ${PORTNAME}-${PORTVERSION}-without-extensions-src MAINTAINER= cartwright@asu.edu COMMENT= Multiple alignment program for amino acid or nucleotide sequences +WWW= https://mafft.cbrc.jp/alignment/software/ LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/license diff --git a/biology/mapm3/Makefile b/biology/mapm3/Makefile index f5dd480e8d19..8350c70b8b2d 100644 --- a/biology/mapm3/Makefile +++ b/biology/mapm3/Makefile @@ -10,6 +10,7 @@ DISTNAME= mapm3-source MAINTAINER= tphilipp@potion-studios.com COMMENT= Constructs linkage maps of markers segregating in experimental crosses +WWW= http://www.broad.mit.edu/ftp/distribution/software/mapmaker3/ LICENSE= MAPMAKER LICENSE_NAME= Whitehead Institute Mapmaker license diff --git a/biology/migrate/Makefile b/biology/migrate/Makefile index 4eabb90c1780..7301261ce15f 100644 --- a/biology/migrate/Makefile +++ b/biology/migrate/Makefile @@ -6,6 +6,7 @@ DISTNAME= ${PORTNAME}-${PORTVERSION}.src MAINTAINER= ports@FreeBSD.org COMMENT= Program to estimate population sizes and migration rates +WWW= https://popgen.sc.fsu.edu/Migrate/Migrate-n.html BROKEN_armv6= fails to build: make[2]: cannot open makefile BROKEN_armv7= fails to build: make[2]: cannot open makefile diff --git a/biology/minimap2/Makefile b/biology/minimap2/Makefile index 0c19edf07eb9..83084fd86a16 100644 --- a/biology/minimap2/Makefile +++ b/biology/minimap2/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Pairwise aligner for genomic and spliced nucleotide sequences +WWW= https://github.com/lh3/minimap2 LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE.txt diff --git a/biology/mmseqs2/Makefile b/biology/mmseqs2/Makefile index 43ff168de33a..0595f54412d7 100644 --- a/biology/mmseqs2/Makefile +++ b/biology/mmseqs2/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Ultra fast and sensitive sequence search and clustering suite +WWW= https://github.com/soedinglab/MMseqs2 LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE.md diff --git a/biology/molden/Makefile b/biology/molden/Makefile index 6cebb3bd3d3e..f16308ecc3e3 100644 --- a/biology/molden/Makefile +++ b/biology/molden/Makefile @@ -7,6 +7,7 @@ DISTNAME= ${PORTNAME}${DISTVERSION} MAINTAINER= jmd@FreeBSD.org COMMENT= Display molecular orbitals and electron densities in 2D and 3D +WWW= https://www.theochem.ru.nl/molden/ LICENSE= Molden LICENSE_NAME= Molden License diff --git a/biology/mothur/Makefile b/biology/mothur/Makefile index 709de5866a24..4a8a6aa6cd57 100644 --- a/biology/mothur/Makefile +++ b/biology/mothur/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org COMMENT= Software for bioinformatics of the microbial ecology community +WWW= https://www.mothur.org/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE.md diff --git a/biology/mrbayes/Makefile b/biology/mrbayes/Makefile index 938936e8122a..0d5b9c070f20 100644 --- a/biology/mrbayes/Makefile +++ b/biology/mrbayes/Makefile @@ -6,6 +6,7 @@ CATEGORIES= biology MAINTAINER= mzaki@e-mail.ne.jp COMMENT= Bayesian inference of phylogeny +WWW= https://nbisweden.github.io/MrBayes/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING diff --git a/biology/mummer/Makefile b/biology/mummer/Makefile index 7291f81fe088..59288a1f8ca3 100644 --- a/biology/mummer/Makefile +++ b/biology/mummer/Makefile @@ -7,6 +7,7 @@ CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org COMMENT= Modular system for rapid whole genome alignment +WWW= http://mummer.sourceforge.net/ LICENSE= ART10 LICENSE_FILE= ${WRKSRC}/LICENSE.md diff --git a/biology/muscle/Makefile b/biology/muscle/Makefile index a25d56907552..dd6b31a9a07f 100644 --- a/biology/muscle/Makefile +++ b/biology/muscle/Makefile @@ -6,6 +6,7 @@ DISTNAME= ${PORTNAME}_src_${PORTVERSION} MAINTAINER= mzaki@e-mail.ne.jp COMMENT= MUltiple Sequence Comparison by Log-Expectation +WWW= https://www.drive5.com/muscle/ LICENSE= PD diff --git a/biology/ncbi-blast+/Makefile b/biology/ncbi-blast+/Makefile index 84b1e49a3b8c..c044de67416a 100644 --- a/biology/ncbi-blast+/Makefile +++ b/biology/ncbi-blast+/Makefile @@ -8,6 +8,7 @@ DISTNAME= ncbi-blast-${PORTVERSION}+-src MAINTAINER= jwb@FreeBSD.org COMMENT= NCBI implementation of Basic Local Alignment Search Tool +WWW= http://blast.ncbi.nlm.nih.gov LICENSE= PD LICENSE_FILE= ${WRKSRC}/scripts/projects/blast/LICENSE diff --git a/biology/ncbi-cxx-toolkit/Makefile b/biology/ncbi-cxx-toolkit/Makefile index 56ecf79ece1d..a01b30ef9411 100644 --- a/biology/ncbi-cxx-toolkit/Makefile +++ b/biology/ncbi-cxx-toolkit/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology science devel MAINTAINER= yuri@FreeBSD.org COMMENT= NCBI C++ Toolkit +WWW= https://ncbi.github.io/cxx-toolkit/ LICENSE= PD LICENSE_FILE= ${WRKSRC}/doc/public/LICENSE diff --git a/biology/ncbi-entrez-direct/Makefile b/biology/ncbi-entrez-direct/Makefile index dc1872c2876f..06dab7ff7e5a 100644 --- a/biology/ncbi-entrez-direct/Makefile +++ b/biology/ncbi-entrez-direct/Makefile @@ -8,6 +8,7 @@ DIST_SUBDIR= edirect-${PORTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= Access to the NCBI's suite of interconnected databases +WWW= https://www.ncbi.nlm.nih.gov/books/NBK179288/ LICENSE= PD diff --git a/biology/ncbi-toolkit/Makefile b/biology/ncbi-toolkit/Makefile index a4d1205ea021..5a714ceec88b 100644 --- a/biology/ncbi-toolkit/Makefile +++ b/biology/ncbi-toolkit/Makefile @@ -8,6 +8,7 @@ DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= NCBI development toolkit, including BLAST 2 and GenBank/Entrez support +WWW= https://www.ncbi.nlm.nih.gov/IEB/ToolBox/MainPage/index.html LIB_DEPENDS= libfontconfig.so:x11-fonts/fontconfig \ libgmp.so:math/gmp \ diff --git a/biology/ncbi-vdb/Makefile b/biology/ncbi-vdb/Makefile index 28bc8b5f05b8..1ae608087727 100644 --- a/biology/ncbi-vdb/Makefile +++ b/biology/ncbi-vdb/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= mzaki@niid.go.jp COMMENT= NCBI's virtualized back-end for accessing Sequence Read Archive +WWW= https://github.com/ncbi/ncbi-vdb/wiki LICENSE= PD LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/ngs-sdk/Makefile b/biology/ngs-sdk/Makefile index 3eadeb6059a9..d93236ccc6f6 100644 --- a/biology/ngs-sdk/Makefile +++ b/biology/ngs-sdk/Makefile @@ -5,6 +5,7 @@ PKGNAMESUFFIX= -sdk MAINTAINER= yuri@FreeBSD.org COMMENT= Tools and libraries for using data in the INSDC Sequence Read Archives +WWW= https://github.com/ncbi/ngs LICENSE= PD LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/p5-AcePerl/Makefile b/biology/p5-AcePerl/Makefile index 6d14329a8661..287a32515731 100644 --- a/biology/p5-AcePerl/Makefile +++ b/biology/p5-AcePerl/Makefile @@ -7,6 +7,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= perl@FreeBSD.org COMMENT= Perl5 interface to the ACEDB genome database system +WWW= https://metacpan.org/release/AcePerl LICENSE= ART10 GPLv1+ LICENSE_COMB= dual diff --git a/biology/p5-Bio-ASN1-EntrezGene/Makefile b/biology/p5-Bio-ASN1-EntrezGene/Makefile index 2f7344e1861f..54c77498bcf0 100644 --- a/biology/p5-Bio-ASN1-EntrezGene/Makefile +++ b/biology/p5-Bio-ASN1-EntrezGene/Makefile @@ -8,6 +8,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= sunpoet@FreeBSD.org COMMENT= Regular expression-based Perl Parser for NCBI Entrez Gene +WWW= https://metacpan.org/release/Bio-ASN1-EntrezGene LICENSE= ART10 GPLv1+ LICENSE_COMB= dual diff --git a/biology/p5-Bio-Cluster/Makefile b/biology/p5-Bio-Cluster/Makefile index 16d13aec2e56..bf526b8497d3 100644 --- a/biology/p5-Bio-Cluster/Makefile +++ b/biology/p5-Bio-Cluster/Makefile @@ -7,6 +7,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= sunpoet@FreeBSD.org COMMENT= BioPerl cluster modules +WWW= https://metacpan.org/release/Bio-Cluster LICENSE= ART10 GPLv1+ LICENSE_COMB= dual diff --git a/biology/p5-Bio-Coordinate/Makefile b/biology/p5-Bio-Coordinate/Makefile index 3939e30416b9..e3541ac7ac2b 100644 --- a/biology/p5-Bio-Coordinate/Makefile +++ b/biology/p5-Bio-Coordinate/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= sunpoet@FreeBSD.org COMMENT= Modules for working with biological coordinates +WWW= https://metacpan.org/release/Bio-Coordinate LICENSE= ART10 GPLv1+ LICENSE_COMB= dual diff --git a/biology/p5-Bio-DB-EMBL/Makefile b/biology/p5-Bio-DB-EMBL/Makefile index 4e51f2858eab..107045db80c4 100644 --- a/biology/p5-Bio-DB-EMBL/Makefile +++ b/biology/p5-Bio-DB-EMBL/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= sunpoet@FreeBSD.org COMMENT= Database object interface for EMBL entry retrieval +WWW= https://metacpan.org/release/Bio-DB-EMBL LICENSE= ART10 GPLv1+ LICENSE_COMB= dual diff --git a/biology/p5-Bio-DB-NCBIHelper/Makefile b/biology/p5-Bio-DB-NCBIHelper/Makefile index 2b2db49a839a..54557aa452ad 100644 --- a/biology/p5-Bio-DB-NCBIHelper/Makefile +++ b/biology/p5-Bio-DB-NCBIHelper/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= sunpoet@FreeBSD.org COMMENT= Collection of routines useful for queries to NCBI databases +WWW= https://metacpan.org/release/Bio-DB-NCBIHelper LICENSE= ART10 GPLv1+ LICENSE_COMB= dual diff --git a/biology/p5-Bio-Das-Lite/Makefile b/biology/p5-Bio-Das-Lite/Makefile index 6894428ae4d2..c4dee3e28fc5 100644 --- a/biology/p5-Bio-Das-Lite/Makefile +++ b/biology/p5-Bio-Das-Lite/Makefile @@ -7,6 +7,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= perl@FreeBSD.org COMMENT= Perl extension for the DAS (HTTP+XML) Protocol +WWW= https://metacpan.org/release/Bio-Das-Lite LICENSE= ART10 GPLv1+ LICENSE_COMB= dual diff --git a/biology/p5-Bio-Das/Makefile b/biology/p5-Bio-Das/Makefile index 3e2c3bcec1df..40e614c5b9da 100644 --- a/biology/p5-Bio-Das/Makefile +++ b/biology/p5-Bio-Das/Makefile @@ -7,6 +7,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= perl@FreeBSD.org COMMENT= Client-side library for Distributed Genome Annotation System +WWW= https://metacpan.org/release/Bio-Das LICENSE= ART10 GPLv1+ LICENSE_COMB= dual diff --git a/biology/p5-Bio-FeatureIO/Makefile b/biology/p5-Bio-FeatureIO/Makefile index 832146b6a889..64d0ec0e3687 100644 --- a/biology/p5-Bio-FeatureIO/Makefile +++ b/biology/p5-Bio-FeatureIO/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= sunpoet@FreeBSD.org COMMENT= Handler for FeatureIO +WWW= https://metacpan.org/release/Bio-FeatureIO LICENSE= ART10 GPLv1+ LICENSE_COMB= dual diff --git a/biology/p5-Bio-GFF3/Makefile b/biology/p5-Bio-GFF3/Makefile index 9b5ab4b8b60f..764bafe929f6 100644 --- a/biology/p5-Bio-GFF3/Makefile +++ b/biology/p5-Bio-GFF3/Makefile @@ -7,6 +7,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= perl@FreeBSD.org COMMENT= Fast low-level functions for parsing and formatting GFF3 +WWW= https://metacpan.org/release/Bio-GFF3 LICENSE= ART10 GPLv1+ LICENSE_COMB= dual diff --git a/biology/p5-Bio-Glite/Makefile b/biology/p5-Bio-Glite/Makefile index f667ab8a9da7..4dad9a47d1b3 100644 --- a/biology/p5-Bio-Glite/Makefile +++ b/biology/p5-Bio-Glite/Makefile @@ -7,6 +7,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= perl@FreeBSD.org COMMENT= Perl Interface to G-language +WWW= https://metacpan.org/release/Bio-Glite BUILD_DEPENDS= ${RUN_DEPENDS} RUN_DEPENDS= p5-libwww>=5:www/p5-libwww diff --git a/biology/p5-Bio-Graphics/Makefile b/biology/p5-Bio-Graphics/Makefile index c064a7ce692a..1c3eace8eb44 100644 --- a/biology/p5-Bio-Graphics/Makefile +++ b/biology/p5-Bio-Graphics/Makefile @@ -7,6 +7,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= perl@FreeBSD.org COMMENT= Generate GD Images of Bio::Seq Objects +WWW= https://metacpan.org/release/Bio-Graphics LICENSE= ART10 GPLv1+ LICENSE_COMB= dual diff --git a/biology/p5-Bio-MAGETAB/Makefile b/biology/p5-Bio-MAGETAB/Makefile index 2c4878e13c42..c4fb02ed6956 100644 --- a/biology/p5-Bio-MAGETAB/Makefile +++ b/biology/p5-Bio-MAGETAB/Makefile @@ -7,6 +7,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= perl@FreeBSD.org COMMENT= Data model and utility API for the MAGE-TAB format +WWW= https://metacpan.org/release/Bio-MAGETAB LICENSE= GPLv2 diff --git a/biology/p5-Bio-NEXUS/Makefile b/biology/p5-Bio-NEXUS/Makefile index f5d5e9044614..9bd1470cf23b 100644 --- a/biology/p5-Bio-NEXUS/Makefile +++ b/biology/p5-Bio-NEXUS/Makefile @@ -7,6 +7,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= perl@FreeBSD.org COMMENT= Object-oriented Perl API for the NEXUS file format +WWW= https://metacpan.org/release/Bio-NEXUS BUILD_DEPENDS= ${RUN_DEPENDS} RUN_DEPENDS= p5-Clone-PP>=1.02:devel/p5-Clone-PP diff --git a/biology/p5-Bio-Phylo/Makefile b/biology/p5-Bio-Phylo/Makefile index bbf990789764..61093e52c484 100644 --- a/biology/p5-Bio-Phylo/Makefile +++ b/biology/p5-Bio-Phylo/Makefile @@ -7,6 +7,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= perl@FreeBSD.org COMMENT= Phylogenetic analysis using Perl +WWW= https://metacpan.org/release/Bio-Phylo LICENSE= ART10 GPLv1+ LICENSE_COMB= dual diff --git a/biology/p5-Bio-SCF/Makefile b/biology/p5-Bio-SCF/Makefile index aa170c454702..88685f19c21b 100644 --- a/biology/p5-Bio-SCF/Makefile +++ b/biology/p5-Bio-SCF/Makefile @@ -7,6 +7,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= wen@FreeBSD.org COMMENT= Read and Update SCF Chromatographic Sequence Files +WWW= https://metacpan.org/release/Bio-SCF LICENSE= ART10 GPLv1+ LICENSE_COMB= dual diff --git a/biology/p5-Bio-Variation/Makefile b/biology/p5-Bio-Variation/Makefile index 55008e2cf0cf..3db6be6b6934 100644 --- a/biology/p5-Bio-Variation/Makefile +++ b/biology/p5-Bio-Variation/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= sunpoet@FreeBSD.org COMMENT= BioPerl variation-related functionality +WWW= https://metacpan.org/release/Bio-Variation LICENSE= ART10 GPLv1+ LICENSE_COMB= dual diff --git a/biology/p5-BioPerl-Run/Makefile b/biology/p5-BioPerl-Run/Makefile index 833e05a4b17b..61bdf13df294 100644 --- a/biology/p5-BioPerl-Run/Makefile +++ b/biology/p5-BioPerl-Run/Makefile @@ -7,6 +7,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= sunpoet@FreeBSD.org COMMENT= Wrapper modules for common bioinformatics tools +WWW= https://github.com/bioperl/bioperl-run LICENSE= ART10 GPLv1+ LICENSE_COMB= dual diff --git a/biology/p5-BioPerl/Makefile b/biology/p5-BioPerl/Makefile index cb5e0bc2ac95..287a930aa726 100644 --- a/biology/p5-BioPerl/Makefile +++ b/biology/p5-BioPerl/Makefile @@ -9,6 +9,7 @@ DISTNAME= ${PORTNAME}-${PORTVERSION:R}${PORTVERSION:E:S|00|.|g} MAINTAINER= sunpoet@FreeBSD.org COMMENT= Collection of Perl modules for bioinformatics +WWW= https://bioperl.org/ LICENSE= ART10 GPLv1+ LICENSE_COMB= dual diff --git a/biology/p5-TrimGalore/Makefile b/biology/p5-TrimGalore/Makefile index b3de61f2fe99..1f777c47af7a 100644 --- a/biology/p5-TrimGalore/Makefile +++ b/biology/p5-TrimGalore/Makefile @@ -5,6 +5,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= jwb@FreeBSD.org COMMENT= Wrapper around Cutadapt and FastQC for adapter and quality trimming +WWW= https://github.com/FelixKrueger/TrimGalore LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/p5-transdecoder/Makefile b/biology/p5-transdecoder/Makefile index 4764a26a1b4f..0c63d4b66408 100644 --- a/biology/p5-transdecoder/Makefile +++ b/biology/p5-transdecoder/Makefile @@ -7,6 +7,7 @@ PKGNAMEPREFIX= p5- MAINTAINER= jwb@FreeBSD.org COMMENT= Identify candidate coding regions within transcript sequences +WWW= https://transdecoder.github.io/ LICENSE= BSD3CLAUSE diff --git a/biology/paml/Makefile b/biology/paml/Makefile index d0f49022b3f7..7286939f9132 100644 --- a/biology/paml/Makefile +++ b/biology/paml/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jrm@FreeBSD.org COMMENT= Phylogenetic Analysis by Maximum Likelihood (PAML) +WWW= http://abacus.gene.ucl.ac.uk/software/paml.html LICENSE= GPLv3 diff --git a/biology/pbbam/Makefile b/biology/pbbam/Makefile index 5b3957a4d0ff..a1fbf997cc8c 100644 --- a/biology/pbbam/Makefile +++ b/biology/pbbam/Makefile @@ -7,6 +7,7 @@ CATEGORIES= biology # See https://github.com/PacificBiosciences/ccs. MAINTAINER= ports@FreeBSD.org COMMENT= PacBio BAM C++ library, with SWIG bindings +WWW= https://github.com/PacificBiosciences/pbbam LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt diff --git a/biology/pbseqan/Makefile b/biology/pbseqan/Makefile index 36aa16e34d37..98b56c5e51e2 100644 --- a/biology/pbseqan/Makefile +++ b/biology/pbseqan/Makefile @@ -6,6 +6,7 @@ CATEGORIES= biology # See https://github.com/PacificBiosciences/ccs. MAINTAINER= ports@FreeBSD.org COMMENT= Pacific Biosciences patched and stripped down SeqAn +WWW= https://github.com/PacificBiosciences/seqan LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/peak-classifier/Makefile b/biology/peak-classifier/Makefile index 315d5a7f65ec..a5eafb536067 100644 --- a/biology/peak-classifier/Makefile +++ b/biology/peak-classifier/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Classify ChIP/ATAC-Seq peaks based on features provided in a GFF +WWW= https://github.com/auerlab/peak-classifier LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/pear-merger/Makefile b/biology/pear-merger/Makefile index 6a4544756905..4d9dcd810e22 100644 --- a/biology/pear-merger/Makefile +++ b/biology/pear-merger/Makefile @@ -9,6 +9,7 @@ DISTNAME= ${PORTNAME}_${PORTVERSION}_src_all MAINTAINER= jwb@FreeBSD.org COMMENT= Memory-efficient and highly accurate paired-end read merger +WWW= https://sco.h-its.org/exelixis/web/software/pear/ LICENSE= CC-BY-NC-SA-3.0 diff --git a/biology/phrap/Makefile b/biology/phrap/Makefile index fa42c1f542a9..813ba478d1cc 100644 --- a/biology/phrap/Makefile +++ b/biology/phrap/Makefile @@ -7,6 +7,7 @@ DIST_SUBDIR= ${PORTNAME} MAINTAINER= mzaki@m.u-tokyo.ac.jp COMMENT= Program for assembling shotgun DNA sequence data +WWW= http://www.phrap.org/phredphrapconsed.html # Converted from RESTRICTED LICENSE= PHRAP diff --git a/biology/phred/Makefile b/biology/phred/Makefile index 4f095b20f7b0..3a5341af8236 100644 --- a/biology/phred/Makefile +++ b/biology/phred/Makefile @@ -7,6 +7,7 @@ EXTRACT_SUFX= .tar.Z MAINTAINER= mzaki@m.u-tokyo.ac.jp COMMENT= Base calling and quality value assignment on DNA sequencing +WWW= http://www.phrap.org/phredphrapconsed.html # Converted from RESTRICTED LICENSE= PHRED diff --git a/biology/phyml/Makefile b/biology/phyml/Makefile index 78ca8bf9f334..fc4d36b518b9 100644 --- a/biology/phyml/Makefile +++ b/biology/phyml/Makefile @@ -6,6 +6,7 @@ CATEGORIES= biology MAINTAINER= ports@FreeBSD.org COMMENT= Simple, fast, and accurate algorithm to estimate large phylogenies +WWW= https://github.com/stephaneguindon/phyml LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING diff --git a/biology/picard-tools/Makefile b/biology/picard-tools/Makefile index f086f83ca177..5efedead9ca7 100644 --- a/biology/picard-tools/Makefile +++ b/biology/picard-tools/Makefile @@ -8,6 +8,7 @@ EXTRACT_SUFX= .jar MAINTAINER= jwb@FreeBSD.org COMMENT= CLI tools for manipulating high-throughput sequencing (HTS) data +WWW= https://broadinstitute.github.io/picard/ LICENSE= MIT diff --git a/biology/plink/Makefile b/biology/plink/Makefile index 46cf662f316e..93e0c5cffe0b 100644 --- a/biology/plink/Makefile +++ b/biology/plink/Makefile @@ -6,6 +6,7 @@ CATEGORIES= biology MAINTAINER= mzaki@e-mail.ne.jp COMMENT= Whole genome association analysis toolset +WWW= https://www.cog-genomics.org/plink/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/pooler/Makefile b/biology/pooler/Makefile index 203f2a38afec..82e5584e2c43 100644 --- a/biology/pooler/Makefile +++ b/biology/pooler/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= ssb22@cam.ac.uk COMMENT= Optimise DNA sequencing primer-set combinations +WWW= https://ssb22.user.srcf.net/pooler/ LICENSE= APACHE20 LICENSE_FILE= ${WRKDIR}/${GH_PROJECT}-${PORTVERSION}/LICENSE diff --git a/biology/primer3/Makefile b/biology/primer3/Makefile index 1016ab451663..99a704ffc353 100644 --- a/biology/primer3/Makefile +++ b/biology/primer3/Makefile @@ -6,6 +6,7 @@ DISTNAME= ${PORTNAME}-src-${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= Primer3 helps to choose primers for PCR reactions +WWW= http://www-genome.wi.mit.edu/genome_software/other/primer3.html LICENSE= GPLv2 diff --git a/biology/prodigal/Makefile b/biology/prodigal/Makefile index 95d7e0ac9d38..7be25f4fd900 100644 --- a/biology/prodigal/Makefile +++ b/biology/prodigal/Makefile @@ -6,6 +6,7 @@ CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org COMMENT= Protein-coding gene prediction for prokaryotic genomes +WWW= https://github.com/hyattpd/Prodigal LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/prodigy-lig/Makefile b/biology/prodigy-lig/Makefile index 634a2cf7575d..18e942dffec0 100644 --- a/biology/prodigy-lig/Makefile +++ b/biology/prodigy-lig/Makefile @@ -7,6 +7,7 @@ CATEGORIES= biology python MAINTAINER= yuri@FreeBSD.org COMMENT= Prediction of protein-small molecule binding affinities +WWW= https://nestor.science.uu.nl/prodigy/lig LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/protomol/Makefile b/biology/protomol/Makefile index 4582fe9b276d..a0dd9ebea947 100644 --- a/biology/protomol/Makefile +++ b/biology/protomol/Makefile @@ -7,6 +7,7 @@ DISTFILES= ${DISTNAME}-tar.gz MAINTAINER= ports@FreeBSD.org COMMENT= OO, component based, framework for molecular dynamics (MD) simulations +WWW= http://protomol.sourceforge.net/ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/py-Genesis-PyAPI/Makefile b/biology/py-Genesis-PyAPI/Makefile index c275c9d6770d..04b16cf9205a 100644 --- a/biology/py-Genesis-PyAPI/Makefile +++ b/biology/py-Genesis-PyAPI/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= API for the Genesis platform for genetics information processing +WWW= https://github.com/genialis/genesis-pyapi/ LICENSE= APACHE20 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/py-PySCeS/Makefile b/biology/py-PySCeS/Makefile index 34201c8b0146..22d55f31307b 100644 --- a/biology/py-PySCeS/Makefile +++ b/biology/py-PySCeS/Makefile @@ -7,6 +7,7 @@ DISTNAME= ${PORTNAME:tl}-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Python Simulator for Cellular Systems +WWW= http://pysces.sourceforge.net/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENCE.txt diff --git a/biology/py-bcbio-gff/Makefile b/biology/py-bcbio-gff/Makefile index b08f6d36f7f2..3896a0f19381 100644 --- a/biology/py-bcbio-gff/Makefile +++ b/biology/py-bcbio-gff/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Read and write Generic Feature Format (GFF) with Biopython integration +WWW= https://pypi.python.org/project/bcbio-gff/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/py-biom-format/Makefile b/biology/py-biom-format/Makefile index 6823ba1326fa..59744dee9ef6 100644 --- a/biology/py-biom-format/Makefile +++ b/biology/py-biom-format/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jrm@FreeBSD.org COMMENT= Biological Observation Matrix (BIOM) Format Project +WWW= https://biom-format.org/ LICENSE= BSD3CLAUSE diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile index a6c08b6e3e2a..9c02066adae9 100644 --- a/biology/py-biopython/Makefile +++ b/biology/py-biopython/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= mauricio@arareko.net COMMENT= Collection of Python modules for bioinformatics +WWW= https://biopython.org/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.rst diff --git a/biology/py-bx-python/Makefile b/biology/py-bx-python/Makefile index 191baf3ad0e8..9221be8cbff4 100644 --- a/biology/py-bx-python/Makefile +++ b/biology/py-bx-python/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Python module for reading, manipulating and writing genomic data sets +WWW= https://github.com/bxlab/bx-python LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/py-crossmap/Makefile b/biology/py-crossmap/Makefile index ba952b7d14c9..4a0f915b3702 100644 --- a/biology/py-crossmap/Makefile +++ b/biology/py-crossmap/Makefile @@ -7,6 +7,7 @@ DISTNAME= CrossMap-${DISTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= Lift over genomics coordinates between assemblies +WWW= https://pypi.python.org/pypi/crossmap LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE.txt diff --git a/biology/py-cutadapt/Makefile b/biology/py-cutadapt/Makefile index 89cf0f128cca..af97b1bf55c2 100644 --- a/biology/py-cutadapt/Makefile +++ b/biology/py-cutadapt/Makefile @@ -7,6 +7,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Trim adapters from high-throughput sequencing reads +WWW= https://pypi.org/project/cutadapt/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/py-deeptools/Makefile b/biology/py-deeptools/Makefile index fb7dd40ad021..1cd477dded81 100644 --- a/biology/py-deeptools/Makefile +++ b/biology/py-deeptools/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= User-friendly tools for exploring deep-sequencing data +WWW= https://github.com/deeptools/deepTools LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt diff --git a/biology/py-deeptoolsintervals/Makefile b/biology/py-deeptoolsintervals/Makefile index e6ebc1066803..d1410ed790a1 100644 --- a/biology/py-deeptoolsintervals/Makefile +++ b/biology/py-deeptoolsintervals/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Python interface for deepTools interval trees +WWW= https://github.com/deeptools/deeptools_intervals LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/py-dna-features-viewer/Makefile b/biology/py-dna-features-viewer/Makefile index 851cde8f7f4d..9c368885c5f5 100644 --- a/biology/py-dna-features-viewer/Makefile +++ b/biology/py-dna-features-viewer/Makefile @@ -7,6 +7,7 @@ DISTNAME= dna_features_viewer-${PORTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= Python library to visualize DNA features, e.g. GenBank or Gff files +WWW= https://pypi.python.org/project/dna-features-viewer/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENCE.txt diff --git a/biology/py-dnaio/Makefile b/biology/py-dnaio/Makefile index 685d4e5f358c..dea08da8fb3e 100644 --- a/biology/py-dnaio/Makefile +++ b/biology/py-dnaio/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Read and write FASTQ and FASTA +WWW= https://pypi.python.org/pypi/dnaio LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/py-ete3/Makefile b/biology/py-ete3/Makefile index 4cbb74719c54..4a4f6eae5e67 100644 --- a/biology/py-ete3/Makefile +++ b/biology/py-ete3/Makefile @@ -7,6 +7,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Framework for the analysis and visualization of trees +WWW= http://etetoolkit.org/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/py-gffutils/Makefile b/biology/py-gffutils/Makefile index 124bb7003382..c5b2a093e0e6 100644 --- a/biology/py-gffutils/Makefile +++ b/biology/py-gffutils/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Work with GFF and GTF files in a flexible database framework +WWW= https://github.com/daler/gffutils LICENSE= MIT diff --git a/biology/py-goatools/Makefile b/biology/py-goatools/Makefile index c2b222f46835..7a6efe69363d 100644 --- a/biology/py-goatools/Makefile +++ b/biology/py-goatools/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Tools for processing and visualizing Gene Ontology terms +WWW= https://pypi.python.org/pypi/goatools LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/py-gtfparse/Makefile b/biology/py-gtfparse/Makefile index e6660fc52287..7cfb40748b3e 100644 --- a/biology/py-gtfparse/Makefile +++ b/biology/py-gtfparse/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Parsing tools for GTF (gene transfer format) files +WWW= https://github.com/openvax/gtfparse LICENSE= APACHE20 diff --git a/biology/py-hits/Makefile b/biology/py-hits/Makefile index 82b38c228994..78f640ffe647 100644 --- a/biology/py-hits/Makefile +++ b/biology/py-hits/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Utilities for processing high-throughput sequencing experiments +WWW= https://github.com/jeffhussmann/hits LICENSE= GPLv3 diff --git a/biology/py-libnuml/Makefile b/biology/py-libnuml/Makefile index 23f0d8d71f9d..6a4099d85b9d 100644 --- a/biology/py-libnuml/Makefile +++ b/biology/py-libnuml/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Numerical Markup Language for Python +WWW= https://github.com/NuML/NuML LICENSE= LGPL21 diff --git a/biology/py-libsedml/Makefile b/biology/py-libsedml/Makefile index b969a095deb0..6b8e59cf0a3e 100644 --- a/biology/py-libsedml/Makefile +++ b/biology/py-libsedml/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= SED-ML library for Python +WWW= https://github.com/fbergmann/libSEDML LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/../../../LICENSE.txt diff --git a/biology/py-loompy/Makefile b/biology/py-loompy/Makefile index 91a46f6a3428..5c3f7a1929e6 100644 --- a/biology/py-loompy/Makefile +++ b/biology/py-loompy/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Work with .loom files for single-cell RNA-seq data +WWW= https://loompy.org/ LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/py-macs2/Makefile b/biology/py-macs2/Makefile index 2b363cc7d941..d24b07a6e3b8 100644 --- a/biology/py-macs2/Makefile +++ b/biology/py-macs2/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Identify transcription factor binding sites +WWW= https://github.com/taoliu/MACS LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/py-mrcfile/Makefile b/biology/py-mrcfile/Makefile index 913473bf89ed..9ad5ea1a08b5 100644 --- a/biology/py-mrcfile/Makefile +++ b/biology/py-mrcfile/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= MRC file I/O library which is used in structural biology +WWW= https://github.com/ccpem/mrcfile LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.txt diff --git a/biology/py-multiqc/Makefile b/biology/py-multiqc/Makefile index 23005cfa7915..4b0a00876054 100644 --- a/biology/py-multiqc/Makefile +++ b/biology/py-multiqc/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Aggregate bioinformatics analysis reports across samples and tools +WWW= https://pypi.python.org/pypi/multiqc LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/py-ont-fast5-api/Makefile b/biology/py-ont-fast5-api/Makefile index 79879d97e612..ea5d333722eb 100644 --- a/biology/py-ont-fast5-api/Makefile +++ b/biology/py-ont-fast5-api/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Interface to HDF5 files in Oxford Nanopore .fast5 format +WWW= https://pypi.python.org/pypi/ont_fast5_api LICENSE= MPL20 LICENSE_FILE= ${WRKSRC}/LICENSE.md diff --git a/biology/py-orange3-bioinformatics/Makefile b/biology/py-orange3-bioinformatics/Makefile index 20198455e1bd..7b97466250ce 100644 --- a/biology/py-orange3-bioinformatics/Makefile +++ b/biology/py-orange3-bioinformatics/Makefile @@ -7,6 +7,7 @@ DISTNAME= Orange3-Bioinformatics-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Orange add-on providing common functionality for bioinformatics +WWW= https://github.com/biolab/orange3-bioinformatics LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/py-orange3-single-cell/Makefile b/biology/py-orange3-single-cell/Makefile index 434fe4035449..fa04f5481e29 100644 --- a/biology/py-orange3-single-cell/Makefile +++ b/biology/py-orange3-single-cell/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Orange add-on for gene expression of single cell data +WWW= https://singlecell.biolab.si/ LICENSE= AGPLv3+ diff --git a/biology/py-pandas-charm/Makefile b/biology/py-pandas-charm/Makefile index 1b556e5faba3..5655d8fcd5d7 100644 --- a/biology/py-pandas-charm/Makefile +++ b/biology/py-pandas-charm/Makefile @@ -7,6 +7,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Library for getting character matrices into and out of pandas +WWW= https://github.com/jmenglund/pandas-charm LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE.txt diff --git a/biology/py-py2bit/Makefile b/biology/py-py2bit/Makefile index 7295e91ed18f..73c9a278c2d2 100644 --- a/biology/py-py2bit/Makefile +++ b/biology/py-py2bit/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Python interface for 2bit packed nucleotide files +WWW= https://github.com/deeptools/py2bit LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE.txt diff --git a/biology/py-pybigwig/Makefile b/biology/py-pybigwig/Makefile index a7c2f9c5321f..39a20d944ecc 100644 --- a/biology/py-pybigwig/Makefile +++ b/biology/py-pybigwig/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Python access to bigWig files using libBigWig +WWW= https://pypi.org/project/pyBigWig/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE.txt diff --git a/biology/py-pyfaidx/Makefile b/biology/py-pyfaidx/Makefile index 98bf5603c93f..0e43ce0af8d2 100644 --- a/biology/py-pyfaidx/Makefile +++ b/biology/py-pyfaidx/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Efficient pythonic random access to fasta subsequences +WWW= https://github.com/mdshw5/pyfaidx LICENSE= BSD3CLAUSE diff --git a/biology/py-pysam/Makefile b/biology/py-pysam/Makefile index 810049593342..e91f94f5d1fd 100644 --- a/biology/py-pysam/Makefile +++ b/biology/py-pysam/Makefile @@ -10,6 +10,7 @@ PATCHFILES= 064c8024395a15024fd590bd90f55f918e15545f.patch:-p1 # backport of sym MAINTAINER= yuri@FreeBSD.org COMMENT= Python module for reading, manipulating and writing genomic data sets +WWW= https://github.com/pysam-developers/pysam LICENSE= MIT LICENSE_FILE= ${WRKSRC}/COPYING diff --git a/biology/py-python-libsbml/Makefile b/biology/py-python-libsbml/Makefile index 33bea5f02f8f..221704edca36 100644 --- a/biology/py-python-libsbml/Makefile +++ b/biology/py-python-libsbml/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= LibSBML Python API +WWW= https://sbml.org/Main_Page LICENSE= LGPL21 diff --git a/biology/py-pywgsim/Makefile b/biology/py-pywgsim/Makefile index 353ec916cbf3..fb3e53fb8dda 100644 --- a/biology/py-pywgsim/Makefile +++ b/biology/py-pywgsim/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= jwb@FreeBSD.org COMMENT= Modified wgsim genomic data simulator +WWW= https://pypi.python.org/pypi/pywgsim LICENSE= MIT diff --git a/biology/py-resdk/Makefile b/biology/py-resdk/Makefile index 68f86a032ef4..56f9e01cf2bb 100644 --- a/biology/py-resdk/Makefile +++ b/biology/py-resdk/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Resolwe SDK to interact with Resolwe server and Resolwe Bioinformatics +WWW= https://github.com/genialis/resolwe-bio-py LICENSE= BSD3CLAUSE diff --git a/biology/py-scikit-bio/Makefile b/biology/py-scikit-bio/Makefile index 0c75ccca8840..d52895fa562b 100644 --- a/biology/py-scikit-bio/Makefile +++ b/biology/py-scikit-bio/Makefile @@ -7,6 +7,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= Data structures, algorithms, educational resources for bioinformatics +WWW= http://scikit-bio.org/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/COPYING.txt diff --git a/biology/py-xenaPython/Makefile b/biology/py-xenaPython/Makefile index b629d7c5d2c7..8eb061c52699 100644 --- a/biology/py-xenaPython/Makefile +++ b/biology/py-xenaPython/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= yuri@FreeBSD.org COMMENT= API for Xena Hub to access genetic information shared through the hub +WWW= https://github.com/ucscXena/xenaPython LICENSE= APACHE20 diff --git a/biology/pyfasta/Makefile b/biology/pyfasta/Makefile index 20663cf666c6..935392ec2724 100644 --- a/biology/pyfasta/Makefile +++ b/biology/pyfasta/Makefile @@ -7,6 +7,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= wen@FreeBSD.org COMMENT= Fast, memory-efficient, pythonic access to fasta sequence files +WWW= https://bitbucket.org/brentp/biostuff/src/ LICENSE= MIT diff --git a/biology/python-nexus/Makefile b/biology/python-nexus/Makefile index 403199c8f651..0c0227d59a7d 100644 --- a/biology/python-nexus/Makefile +++ b/biology/python-nexus/Makefile @@ -6,6 +6,7 @@ PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX} MAINTAINER= wen@FreeBSD.org COMMENT= Generic nexus file format reader for python +WWW= http://simon.net.nz/articles/python-nexus LICENSE= BSD3CLAUSE #LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/rainbow/Makefile b/biology/rainbow/Makefile index a1878eac6988..f6efc6f1fe80 100644 --- a/biology/rainbow/Makefile +++ b/biology/rainbow/Makefile @@ -6,6 +6,7 @@ DISTNAME= rainbow_${PORTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= Efficient clustering and assembling of short reads, especially for RAD +WWW= https://sourceforge.net/projects/bio-rainbow/ LICENSE= GPLv3+ diff --git a/biology/rampler/Makefile b/biology/rampler/Makefile index b5b5fc65314b..0de5760c12fe 100644 --- a/biology/rampler/Makefile +++ b/biology/rampler/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org COMMENT= Standalone module for sampling genomic sequences +WWW= https://github.com/rvaser/rampler LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/readseq/Makefile b/biology/readseq/Makefile index e7d711885e28..af5dafdf3af8 100644 --- a/biology/readseq/Makefile +++ b/biology/readseq/Makefile @@ -9,6 +9,7 @@ EXTRACT_SUFX= .jar MAINTAINER= jwb@FreeBSD.org COMMENT= Read and reformat biosequences, Java command-line version +WWW= https://sourceforge.net/projects/readseq LICENSE= PD diff --git a/biology/recombine/Makefile b/biology/recombine/Makefile index 1a14861eec31..1f3b77b7c7c4 100644 --- a/biology/recombine/Makefile +++ b/biology/recombine/Makefile @@ -7,6 +7,7 @@ DISTNAME= ${PORTNAME}${PORTVERSION}.src.doc MAINTAINER= ports@FreeBSD.org COMMENT= Program to fit population models across sites +WWW= https://evolution.genetics.washington.edu/lamarc/recombine.html USES= shebangfix diff --git a/biology/ruby-bio/Makefile b/biology/ruby-bio/Makefile index 5881427be774..1591a41a08c6 100644 --- a/biology/ruby-bio/Makefile +++ b/biology/ruby-bio/Makefile @@ -8,6 +8,7 @@ DIST_SUBDIR= ruby MAINTAINER= mauricio@arareko.net COMMENT= Integrated environment for Bioinformatics written in Ruby +WWW= http://bioruby.org/ LICENSE= GPLv2 RUBY LICENSE_COMB= dual diff --git a/biology/rubygem-bio-executables/Makefile b/biology/rubygem-bio-executables/Makefile index 81c5dabe5e01..2d0913c0c8ac 100644 --- a/biology/rubygem-bio-executables/Makefile +++ b/biology/rubygem-bio-executables/Makefile @@ -5,6 +5,7 @@ MASTER_SITES= RG MAINTAINER= sunpoet@FreeBSD.org COMMENT= Collection of miscellaneous utilities for bioinformatics +WWW= https://github.com/bioruby/bioruby-executables LICENSE= BSD2CLAUSE RUBY LICENSE_COMB= dual diff --git a/biology/rubygem-bio-old-biofetch-emulator/Makefile b/biology/rubygem-bio-old-biofetch-emulator/Makefile index 38414d8adc15..f3e35ae73d49 100644 --- a/biology/rubygem-bio-old-biofetch-emulator/Makefile +++ b/biology/rubygem-bio-old-biofetch-emulator/Makefile @@ -5,6 +5,7 @@ MASTER_SITES= RG MAINTAINER= sunpoet@FreeBSD.org COMMENT= Emulate Bio::Fetch object +WWW= https://github.com/ngoto/bioruby-old-biofetch-emulator LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE.txt diff --git a/biology/rubygem-bio-shell/Makefile b/biology/rubygem-bio-shell/Makefile index 3fbfc44f0a72..d18fcf757b84 100644 --- a/biology/rubygem-bio-shell/Makefile +++ b/biology/rubygem-bio-shell/Makefile @@ -5,6 +5,7 @@ MASTER_SITES= RG MAINTAINER= sunpoet@FreeBSD.org COMMENT= Command-line interface on BioRuby +WWW= https://github.com/bioruby/bioruby-shell LICENSE= BSD2CLAUSE RUBY LICENSE_COMB= dual diff --git a/biology/rubygem-bio/Makefile b/biology/rubygem-bio/Makefile index 8cdc12018b74..0169e71eac46 100644 --- a/biology/rubygem-bio/Makefile +++ b/biology/rubygem-bio/Makefile @@ -5,6 +5,7 @@ MASTER_SITES= RG MAINTAINER= ruby@FreeBSD.org COMMENT= Integrated environment for Bioinformatics written in Ruby +WWW= http://bioruby.org/ LICENSE= BSD2CLAUSE RUBY LICENSE_COMB= dual diff --git a/biology/sam2pairwise/Makefile b/biology/sam2pairwise/Makefile index dd578353e5a9..411050625902 100644 --- a/biology/sam2pairwise/Makefile +++ b/biology/sam2pairwise/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Show pairwise alignment for each read in a SAM file +WWW= https://github.com/mlafave/sam2pairwise LICENSE= MIT LICENSE_FILE= ${WRKDIR}/${PORTNAME}-${PORTVERSION}/LICENSE diff --git a/biology/samtools/Makefile b/biology/samtools/Makefile index c6f75a0f3396..cbdfaa3b607b 100644 --- a/biology/samtools/Makefile +++ b/biology/samtools/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Tools for manipulating next-generation sequencing data +WWW= https://www.htslib.org/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/scrm/Makefile b/biology/scrm/Makefile index 875f5e2cd257..f75e14f045e0 100644 --- a/biology/scrm/Makefile +++ b/biology/scrm/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org COMMENT= Coalescent simulator for biological sequences +WWW= https://scrm.github.io/ LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/COPYING diff --git a/biology/seaview/Makefile b/biology/seaview/Makefile index 6f2226617efe..0dea6c7a7b48 100644 --- a/biology/seaview/Makefile +++ b/biology/seaview/Makefile @@ -7,6 +7,7 @@ DISTNAME= ${PORTNAME}_${PORTVERSION} MAINTAINER= bofh@FreeBSD.org COMMENT= Multiple DNA/protein sequence alignment editor +WWW= https://doua.prabi.fr/software/seaview LICENSE= GPLv3 diff --git a/biology/seqan-apps/Makefile b/biology/seqan-apps/Makefile index 295d5ab9823c..bbf27aaa5406 100644 --- a/biology/seqan-apps/Makefile +++ b/biology/seqan-apps/Makefile @@ -6,6 +6,7 @@ CATEGORIES= biology MAINTAINER= h2+fbsdports@fsfe.org COMMENT= Official bioinformatic applications based on the SeqAn library +WWW= https://www.seqan.de/ LICENSE= BSD3CLAUSE LGPL3 GPLv3 LICENSE_COMB= multi diff --git a/biology/seqan/Makefile b/biology/seqan/Makefile index f9deb90d8668..dced6aed65a5 100644 --- a/biology/seqan/Makefile +++ b/biology/seqan/Makefile @@ -6,6 +6,7 @@ DISTNAME= ${PORTNAME}-library-${PORTVERSION} MAINTAINER= h2+fbsdports@fsfe.org COMMENT= C++ sequence analysis template library +WWW= https://www.seqan.de/ LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/share/doc/seqan/LICENSE diff --git a/biology/seqan1/Makefile b/biology/seqan1/Makefile index 5031bfcda333..41df12e1622a 100644 --- a/biology/seqan1/Makefile +++ b/biology/seqan1/Makefile @@ -7,6 +7,7 @@ PKGNAMESUFFIX= 1 MAINTAINER= h2+fbsdports@fsfe.org COMMENT= C++ Sequence Analysis Library +WWW= https://www.seqan.de/ LICENSE= BSD3CLAUSE LICENSE_FILE_BSD3CLAUSE= ${WRKSRC}/seqan/LICENSE diff --git a/biology/seqan3/Makefile b/biology/seqan3/Makefile index 61bdef82ecc3..8937dfb0d812 100644 --- a/biology/seqan3/Makefile +++ b/biology/seqan3/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology devel math MAINTAINER= yuri@FreeBSD.org COMMENT= C++ header-only library for biological sequence analysis +WWW= https://github.com/seqan/seqan3 LICENSE= BSD3CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE.md diff --git a/biology/seqio/Makefile b/biology/seqio/Makefile index e6e32142f2c7..c6a10dc21c90 100644 --- a/biology/seqio/Makefile +++ b/biology/seqio/Makefile @@ -7,6 +7,7 @@ DISTNAME= ${PORTNAME} MAINTAINER= ports@FreeBSD.org COMMENT= Set of C functions which can read/write biological sequence files +WWW= https://www.cs.ucdavis.edu/~gusfield/seqio.html WRKSRC= ${WRKDIR}/${PORTNAME}-${PORTVERSION} diff --git a/biology/seqkit/Makefile b/biology/seqkit/Makefile index 4bd3f3e3728b..c9378d00aced 100644 --- a/biology/seqkit/Makefile +++ b/biology/seqkit/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org COMMENT= Cross-platform and ultrafast toolkit for FASTA/Q file manipulation +WWW= https://bioinf.shenwei.me/seqkit/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/seqtk/Makefile b/biology/seqtk/Makefile index c4b0dd5ecab6..6a779dfd93b4 100644 --- a/biology/seqtk/Makefile +++ b/biology/seqtk/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Tool for processing sequences in FASTA/FASTQ format +WWW= https://github.com/lh3/seqtk LICENSE= GPLv2 diff --git a/biology/sigviewer/Makefile b/biology/sigviewer/Makefile index dba6986ee79c..ebea657a8969 100644 --- a/biology/sigviewer/Makefile +++ b/biology/sigviewer/Makefile @@ -7,6 +7,7 @@ CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org COMMENT= Viewing application for biosignals +WWW= https://github.com/cbrnr/sigviewer LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/slclust/Makefile b/biology/slclust/Makefile index b6c220a94935..4d906f1fca07 100644 --- a/biology/slclust/Makefile +++ b/biology/slclust/Makefile @@ -6,6 +6,7 @@ DISTNAME= ${PORTNAME}_02022010 MAINTAINER= jwb@FreeBSD.org COMMENT= Single-linkage clustering with Jaccard similarity +WWW= https://sourceforge.net/projects/slclust/ LICENSE= ART10 diff --git a/biology/smithwaterman/Makefile b/biology/smithwaterman/Makefile index 3c8c0b3c8208..f476f69a416c 100644 --- a/biology/smithwaterman/Makefile +++ b/biology/smithwaterman/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Smith-waterman-gotoh alignment algorithm +WWW= https://github.com/ekg/smithwaterman LICENSE= GPLv2 diff --git a/biology/snpeff/Makefile b/biology/snpeff/Makefile index 830021419708..ac4b81e11561 100644 --- a/biology/snpeff/Makefile +++ b/biology/snpeff/Makefile @@ -7,6 +7,7 @@ DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= Genetic variant annotation and effect prediction toolbox +WWW= http://snpeff.sourceforge.net/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE.md diff --git a/biology/spoa/Makefile b/biology/spoa/Makefile index 8b853e9bc7e3..163a9fb07918 100644 --- a/biology/spoa/Makefile +++ b/biology/spoa/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org COMMENT= C++ implementation of the partial order alignment (POA) algorithm +WWW= https://github.com/rvaser/spoa LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/sra-tools/Makefile b/biology/sra-tools/Makefile index e4ebace60279..77a5b54b0416 100644 --- a/biology/sra-tools/Makefile +++ b/biology/sra-tools/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= NCBI's toolkit for handling data in INSDC Sequence Read Archives +WWW= https://github.com/ncbi/sra-tools/wiki LICENSE= PD LGPL21+ LICENSE_COMB= multi diff --git a/biology/stacks/Makefile b/biology/stacks/Makefile index cbd6bf3912d3..b4301eec2bb7 100644 --- a/biology/stacks/Makefile +++ b/biology/stacks/Makefile @@ -6,6 +6,7 @@ MASTER_SITES= http://catchenlab.life.illinois.edu/stacks/source/ MAINTAINER= jwb@FreeBSD.org COMMENT= Software pipeline for building loci from short-read sequences +WWW= https://catchenlab.life.illinois.edu/stacks/ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/star/Makefile b/biology/star/Makefile index 12f862562221..1cb819872a6f 100644 --- a/biology/star/Makefile +++ b/biology/star/Makefile @@ -5,6 +5,7 @@ PKGNAMEPREFIX= rna- MAINTAINER= jwb@FreeBSD.org COMMENT= Spliced Transcripts Alignment to a Reference +WWW= https://github.com/alexdobin/STAR LICENSE= GPLv3 LICENSE_FILE= ${WRKDIR}/STAR-${DISTVERSION}/LICENSE diff --git a/biology/stringtie/Makefile b/biology/stringtie/Makefile index 5e261632b31c..8341112877d1 100644 --- a/biology/stringtie/Makefile +++ b/biology/stringtie/Makefile @@ -5,6 +5,7 @@ MASTER_SITES= http://ccb.jhu.edu/software/stringtie/dl/ MAINTAINER= mzaki@e-mail.ne.jp COMMENT= Transcript assembly and quantification for RNA-seq +WWW= http://www.ccb.jhu.edu/software/stringtie/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/subread/Makefile b/biology/subread/Makefile index 44ff5508a8dc..f1d4b49106e1 100644 --- a/biology/subread/Makefile +++ b/biology/subread/Makefile @@ -6,6 +6,7 @@ MASTER_SITES= SF/${PORTNAME}/${PORTNAME}-${PORTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= High-performance read alignment, quantification and mutation discovery +WWW= http://bioinf.wehi.edu.au/subread-package/ LICENSE= GPLv3 LICENSE_FILE= ${WRKDIR}/${DISTNAME}/LICENSE diff --git a/biology/tRNAscan-SE/Makefile b/biology/tRNAscan-SE/Makefile index 856c87e66645..75658cb534c0 100644 --- a/biology/tRNAscan-SE/Makefile +++ b/biology/tRNAscan-SE/Makefile @@ -6,6 +6,7 @@ DISTFILES= ${DISTNAME:tl}${EXTRACT_SUFX} MAINTAINER= mzaki@e-mail.ne.jp COMMENT= Searching for tRNA genes in genomic sequence +WWW= http://lowelab.ucsc.edu/tRNAscan-SE/ LICENSE= GPLv3+ LICENSE_FILE= ${WRKSRC}/COPYING diff --git a/biology/tabixpp/Makefile b/biology/tabixpp/Makefile index 688838e66527..17fa18584fea 100644 --- a/biology/tabixpp/Makefile +++ b/biology/tabixpp/Makefile @@ -7,6 +7,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= C++ wrapper to tabix indexer +WWW= https://github.com/ekg/tabixpp LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/taxonkit/Makefile b/biology/taxonkit/Makefile index e2e974adb5c7..587c83fe14cc 100644 --- a/biology/taxonkit/Makefile +++ b/biology/taxonkit/Makefile @@ -6,6 +6,7 @@ CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org COMMENT= Practical and efficient NCBI taxonomy toolkit +WWW= https://bioinf.shenwei.me/taxonkit/ LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/treekin/Makefile b/biology/treekin/Makefile index 333043189b1c..3495feedc09f 100644 --- a/biology/treekin/Makefile +++ b/biology/treekin/Makefile @@ -7,6 +7,7 @@ DISTNAME= Treekin-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Efficient computation of RNA folding dynamics +WWW= https://www.tbi.univie.ac.at/RNA/Treekin/ LICENSE= LatticeLib LICENSE_NAME= LatticeLib Disclaimer and Copyright diff --git a/biology/treepuzzle/Makefile b/biology/treepuzzle/Makefile index 512e11715884..a15ddeaca6dc 100644 --- a/biology/treepuzzle/Makefile +++ b/biology/treepuzzle/Makefile @@ -6,6 +6,7 @@ DISTNAME= tree-puzzle-${PORTVERSION} MAINTAINER= jan.lentfer@web.de COMMENT= Maximum likelihood phylogeny reconstruction using quartets +WWW= http://www.tree-puzzle.de GNU_CONFIGURE= yes PLIST_FILES= bin/puzzle diff --git a/biology/trimadap/Makefile b/biology/trimadap/Makefile index e86383007f5b..6f5a87f07a84 100644 --- a/biology/trimadap/Makefile +++ b/biology/trimadap/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Trim adapter sequences from Illumina data using heuristic rules +WWW= https://github.com/lh3/trimadap LICENSE= GPLv2 diff --git a/biology/trimmomatic/Makefile b/biology/trimmomatic/Makefile index 31fa6b74275e..f2251499f6b5 100644 --- a/biology/trimmomatic/Makefile +++ b/biology/trimmomatic/Makefile @@ -6,6 +6,7 @@ DISTNAME= Trimmomatic-${PORTVERSION} MAINTAINER= jwb@FreeBSD.org COMMENT= Flexible read trimming tool for Illumina NGS data +WWW= http://www.usadellab.org/cms/?page=trimmomatic LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/ucsc-userapps/Makefile b/biology/ucsc-userapps/Makefile index 67dad384dcbe..46070c6bfa77 100644 --- a/biology/ucsc-userapps/Makefile +++ b/biology/ucsc-userapps/Makefile @@ -7,6 +7,7 @@ DISTNAME= userApps.v${PORTVERSION}.src MAINTAINER= jwb@FreeBSD.org COMMENT= Command line tools from the UCSC Genome Browser project +WWW= https://hgdownload.cse.ucsc.edu/admin/exe/ LICENSE= UCSC-GB LICENSE_NAME= UCSC Genome Browser License diff --git a/biology/ugene/Makefile b/biology/ugene/Makefile index 245951aff815..e3122d99ed81 100644 --- a/biology/ugene/Makefile +++ b/biology/ugene/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology science MAINTAINER= h2+fbsdports@fsfe.org COMMENT= Integrated bioinformatics toolkit +WWW= https://ugene.net/ LICENSE= GPLv2+ LICENSE_FILE= ${WRKSRC}/LICENSE.txt diff --git a/biology/unikmer/Makefile b/biology/unikmer/Makefile index e9d69b3c692e..e7af64ca7c18 100644 --- a/biology/unikmer/Makefile +++ b/biology/unikmer/Makefile @@ -6,6 +6,7 @@ CATEGORIES= biology MAINTAINER= yuri@FreeBSD.org COMMENT= Toolkit for nucleic acid k-mer analysis, set operations on k-mers +WWW= https://github.com/shenwei356/unikmer LICENSE= MIT LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/vcf-split/Makefile b/biology/vcf-split/Makefile index 039ddae7ae4d..51f420bf3ac5 100644 --- a/biology/vcf-split/Makefile +++ b/biology/vcf-split/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Split a multi-sample VCF into single-sample VCFs +WWW= https://github.com/auerlab/vcf-split LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/vcf2hap/Makefile b/biology/vcf2hap/Makefile index 39a9ea452c0e..fb903a18c741 100644 --- a/biology/vcf2hap/Makefile +++ b/biology/vcf2hap/Makefile @@ -4,6 +4,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Generate .hap file from VCF for haplohseq +WWW= https://github.com/auerlab/vcf2hap LICENSE= BSD2CLAUSE LICENSE_FILE= ${WRKSRC}/LICENSE diff --git a/biology/vcflib/Makefile b/biology/vcflib/Makefile index 1ab10160d404..1f41ab06b838 100644 --- a/biology/vcflib/Makefile +++ b/biology/vcflib/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= C++ library and CLI tools for parsing and manipulating VCF files +WWW= https://github.com/vcflib/vcflib LICENSE= MIT diff --git a/biology/vcftools/Makefile b/biology/vcftools/Makefile index 6eca3628e6c7..ba3b812a3ed1 100644 --- a/biology/vcftools/Makefile +++ b/biology/vcftools/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Tools for working with VCF genomics files +WWW= https://github.com/vcftools/vcftools LICENSE= LGPL3 diff --git a/biology/velvet/Makefile b/biology/velvet/Makefile index 24863af0ecd5..b93a28cdf203 100644 --- a/biology/velvet/Makefile +++ b/biology/velvet/Makefile @@ -7,6 +7,7 @@ DISTNAME= ${PORTNAME}_${PORTVERSION} MAINTAINER= mzaki@m.u-tokyo.ac.jp COMMENT= Sequence assembler for very short reads +WWW= http://www.ebi.ac.uk/~zerbino/velvet/ ALL_TARGET= default diff --git a/biology/viennarna/Makefile b/biology/viennarna/Makefile index 31558cd140f9..b46cd561764d 100644 --- a/biology/viennarna/Makefile +++ b/biology/viennarna/Makefile @@ -6,6 +6,7 @@ DISTNAME= ViennaRNA-${DISTVERSION} MAINTAINER= yuri@FreeBSD.org COMMENT= Alignment tools for the structural analysis of RNA +WWW= https://github.com/s-will/LocARNA LICENSE= ViennaRNALicense LICENSE_NAME= Vienna RNA License diff --git a/biology/vsearch/Makefile b/biology/vsearch/Makefile index f517400f6e34..99d003441aa3 100644 --- a/biology/vsearch/Makefile +++ b/biology/vsearch/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Versatile open-source tool for metagenomics +WWW= https://github.com/torognes/vsearch LICENSE= GPLv3 LICENSE_FILE= ${WRKSRC}/LICENSE.txt diff --git a/biology/vt/Makefile b/biology/vt/Makefile index 9e5e69141b6d..1805e374602e 100644 --- a/biology/vt/Makefile +++ b/biology/vt/Makefile @@ -5,6 +5,7 @@ CATEGORIES= biology MAINTAINER= jwb@FreeBSD.org COMMENT= Discovers short variants from Next Generation Sequencing data +WWW= https://genome.sph.umich.edu/wiki/Vt LICENSE= MIT diff --git a/biology/wise/Makefile b/biology/wise/Makefile index 357b585df038..c842f27fc678 100644 --- a/biology/wise/Makefile +++ b/biology/wise/Makefile @@ -7,6 +7,7 @@ DISTNAME= ${PORTNAME}${PORTVERSION} MAINTAINER= ports@FreeBSD.org COMMENT= Intelligent algorithms for DNA searches +WWW= http://www.ebi.ac.uk/Wise2/ BUILD_WRKSRC= ${WRKSRC}/src |