BSD Portsbiology/vsearch 2.32.0 FreeBSD
Versatile open-source tool for metagenomics
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- Last update
- Commit
2414383046- License
- GPLv3
- Categories
- biology
- Package size
- 729.5 KiB, 1558.4 KiB installed
Description
VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads.
The aim of this project is to create an alternative to the USEARCH tool developed by Robert C. Edgar (2010).
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | biology/vsearch | 2.32.0 |
| NetBSD | biology/vsearch | 2.29.4 |
| HardenedBSD | biology/vsearch | 2.32.0 |
| GhostBSD | biology/vsearch | 2.32.0 |
Install
Binary package:
pkg install vsearchFrom the ports tree:
cd /usr/ports/biology/vsearch/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= vsearch>0:biology/vsearchPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 2.32.0 | 2.32.0 | - | - | - |
| FreeBSD:14:quarterly | 2.32.0 | 2.32.0 | n/a | - | - |
| FreeBSD:15:latest | 2.32.0 | 2.32.0 | n/a | - | - |
| FreeBSD:15:quarterly | 2.32.0 | 2.32.0 | n/a | n/a | n/a |
| FreeBSD:16:latest | 2.32.0 | 2.32.0 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Build 2
hs-pandoc>0: textproc/hs-pandocbash>0: shells/bash
The full lists below include those, and their dependencies in turn.
Build dependencies 61
- archivers/brotli
- archivers/libdeflate
- archivers/liblz4
- archivers/zstd
- converters/libiconv
- databases/gdbm
- devel/autoconf
- devel/autoconf-switch
- devel/automake
- devel/dbus
- devel/dbus-glib
- devel/gettext-runtime
- devel/glib20
- devel/gmake
- devel/libdaemon
- devel/libevent
- devel/libffi
- devel/libinotify
- devel/m4
- devel/pcre2
- devel/py-packaging
- devel/readline
- dns/libidn
- graphics/jbig2dec
- graphics/jbigkit
- graphics/jpeg-turbo
- graphics/lcms2
- graphics/lerc
- graphics/openjpeg
- graphics/png
- graphics/poppler-data
- graphics/tiff
- lang/perl5.42
- lang/python312
- lang/python315
- math/gmp
- math/mpdecimal
- net/avahi-app
- print/cups
- print/freetype2
- print/ghostscript10
- print/indexinfo
- print/libpaper
- shells/bash
- sysutils/gnome_subr
- textproc/expat2
- textproc/hs-pandoc
- textproc/libxml2
- x11-fonts/fontconfig
- x11-fonts/libfontenc
- x11-fonts/mkfontscale
- x11-fonts/urw-base35-fonts
- x11-toolkits/libXt
- x11/libICE
- x11/libSM
- x11/libX11
- x11/libXau
- x11/libXdmcp
- x11/libXext
- x11/libxcb
- x11/xorgproto
No port depends on this one.
Configuration
No options to configure.
- USES
- autoreconf ghostscript:build gmake localbase
- Service scripts
- none
Files
Manual pages 63
- vsearch(1)
- vsearch-allpairs_global(1)
- vsearch-chimeras_denovo(1)
- vsearch-cigar(5)
- vsearch-cluster_fast(1)
- vsearch-cluster_size(1)
- vsearch-cluster_smallmem(1)
- vsearch-cluster_unoise(1)
- vsearch-cut(1)
- vsearch-derep_fulllength(1)
- vsearch-derep_id(1)
- vsearch-derep_prefix(1)
- vsearch-derep_smallmem(1)
- vsearch-expected_error(7)
- vsearch-fasta(5)
- vsearch-fasta2fastq(1)
- vsearch-fastq(5)
- vsearch-fastq_chars(1)
- vsearch-fastq_convert(1)
- vsearch-fastq_eestats(1)
- vsearch-fastq_eestats2(1)
- vsearch-fastq_filter(1)
- vsearch-fastq_join(1)
- vsearch-fastq_mergepairs(1)
- vsearch-fastq_stats(1)
- vsearch-fastx_filter(1)
- vsearch-fastx_getseq(1)
- vsearch-fastx_getseqs(1)
- vsearch-fastx_getsubseq(1)
- vsearch-fastx_mask(1)
- vsearch-fastx_revcomp(1)
- vsearch-fastx_subsample(1)
- vsearch-fastx_syncpairs(1)
- vsearch-fastx_uniques(1)
- vsearch-help(1)
- vsearch-history(7)
- vsearch-makeudb_usearch(1)
- vsearch-maskfasta(1)
- vsearch-nucleotides(7)
- vsearch-orient(1)
- vsearch-pairwise_alignment_parameters(7)
- vsearch-rereplicate(1)
- vsearch-sam(5)
- vsearch-scramble(1)
- vsearch-search_exact(1)
- vsearch-sff(5)
- vsearch-sff_convert(1)
- vsearch-shuffle(1)
- vsearch-sintax(1)
- vsearch-sortbylength(1)
- vsearch-sortbysize(1)
- vsearch-uchime2_denovo(1)
- vsearch-uchime3_denovo(1)
- vsearch-uchime_denovo(1)
- vsearch-uchime_ref(1)
- vsearch-udb(5)
- vsearch-udb2fasta(1)
- vsearch-udbinfo(1)
- vsearch-udbstats(1)
- vsearch-usearch(7)
- vsearch-usearch_global(1)
- vsearch-userfields(7)
- vsearch-version(1)
pkg-plist 67
- bin/vsearch
- share/bash-completion/completions/vsearch
- share/fish/vendor_completions.d/vsearch.fish
- share/man/man1/vsearch-allpairs_global.1.gz
- share/man/man1/vsearch-chimeras_denovo.1.gz
- share/man/man1/vsearch-cluster_fast.1.gz
- share/man/man1/vsearch-cluster_size.1.gz
- share/man/man1/vsearch-cluster_smallmem.1.gz
- share/man/man1/vsearch-cluster_unoise.1.gz
- share/man/man1/vsearch-cut.1.gz
- share/man/man1/vsearch-derep_fulllength.1.gz
- share/man/man1/vsearch-derep_id.1.gz
- share/man/man1/vsearch-derep_prefix.1.gz
- share/man/man1/vsearch-derep_smallmem.1.gz
- share/man/man1/vsearch-fasta2fastq.1.gz
- share/man/man1/vsearch-fastq_chars.1.gz
- share/man/man1/vsearch-fastq_convert.1.gz
- share/man/man1/vsearch-fastq_eestats.1.gz
- share/man/man1/vsearch-fastq_eestats2.1.gz
- share/man/man1/vsearch-fastq_filter.1.gz
- share/man/man1/vsearch-fastq_join.1.gz
- share/man/man1/vsearch-fastq_mergepairs.1.gz
- share/man/man1/vsearch-fastq_stats.1.gz
- share/man/man1/vsearch-fastx_filter.1.gz
- share/man/man1/vsearch-fastx_getseq.1.gz
- share/man/man1/vsearch-fastx_getseqs.1.gz
- share/man/man1/vsearch-fastx_getsubseq.1.gz
- share/man/man1/vsearch-fastx_mask.1.gz
- share/man/man1/vsearch-fastx_revcomp.1.gz
- share/man/man1/vsearch-fastx_subsample.1.gz
- share/man/man1/vsearch-fastx_syncpairs.1.gz
- share/man/man1/vsearch-fastx_uniques.1.gz
- share/man/man1/vsearch-help.1.gz
- share/man/man1/vsearch-makeudb_usearch.1.gz
- share/man/man1/vsearch-maskfasta.1.gz
- share/man/man1/vsearch-orient.1.gz
- share/man/man1/vsearch-rereplicate.1.gz
- share/man/man1/vsearch-scramble.1.gz
- share/man/man1/vsearch-search_exact.1.gz
- share/man/man1/vsearch-sff_convert.1.gz
- share/man/man1/vsearch-shuffle.1.gz
- share/man/man1/vsearch-sintax.1.gz
- share/man/man1/vsearch-sortbylength.1.gz
- share/man/man1/vsearch-sortbysize.1.gz
- share/man/man1/vsearch-uchime2_denovo.1.gz
- share/man/man1/vsearch-uchime3_denovo.1.gz
- share/man/man1/vsearch-uchime_denovo.1.gz
- share/man/man1/vsearch-uchime_ref.1.gz
- share/man/man1/vsearch-udb2fasta.1.gz
- share/man/man1/vsearch-udbinfo.1.gz
- share/man/man1/vsearch-udbstats.1.gz
- share/man/man1/vsearch-usearch_global.1.gz
- share/man/man1/vsearch-version.1.gz
- share/man/man1/vsearch.1.gz
- share/man/man5/vsearch-cigar.5.gz
- share/man/man5/vsearch-fasta.5.gz
- share/man/man5/vsearch-fastq.5.gz
- share/man/man5/vsearch-sam.5.gz
- share/man/man5/vsearch-sff.5.gz
- share/man/man5/vsearch-udb.5.gz
- share/man/man7/vsearch-expected_error.7.gz
- share/man/man7/vsearch-history.7.gz
- share/man/man7/vsearch-nucleotides.7.gz
- share/man/man7/vsearch-pairwise_alignment_parameters.7.gz
- share/man/man7/vsearch-usearch.7.gz
- share/man/man7/vsearch-userfields.7.gz
- share/zsh/site-functions/_vsearch
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| torognes-vsearch-v2.32.0_GH0.tar.gz | 824198 | aa6fecd099ba4970b2685e41e3a97e04f1317d12cb315870e3acdc1cd6b7fe5d |