diff options
| author | Stefan Eßer <se@FreeBSD.org> | 2022-09-07 23:06:12 +0200 |
|---|---|---|
| committer | Stefan Eßer <se@FreeBSD.org> | 2022-09-07 23:10:59 +0200 |
| commit | b7f05445c00f2625aa19b4154ebcbce5ed2daa52 (patch) | |
| tree | c3b04fc0b07c55f849072e9b35e694f3d8ccf871 /biology | |
| parent | graphics/tesseract: fix build when building from ports (diff) | |
Add WWW entries to port Makefiles
It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.
Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.
There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.
There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.
The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.
Approved by: portmgr (tcberner)
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 |