BSD Ports

biology/bcftools 1.24 FreeBSD

Tools for manipulating next-generation sequencing data

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
2414383046
License
MIT
Categories
biology
Package size
823.4 KiB, 2555.4 KiB installed

Description

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.

In the other systems

SystemPortVersion
FreeBSDbiology/bcftools1.24
NetBSDbiology/bcftools1.21
DragonFlybiology/bcftools1.21

Install

Binary package:

pkg install bcftools

From the ports tree:

cd /usr/ports/biology/bcftools/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	bcftools>0:biology/bcftools

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repositoryaarch64amd64armv6armv7i386
FreeBSD:14:latest1.241.241.16-1.24
FreeBSD:14:quarterly1.241.24n/a-1.24
FreeBSD:15:latest1.241.24n/a-1.22
FreeBSD:15:quarterly1.241.24n/an/an/a
FreeBSD:16:latest1.241.24n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

As this port's Makefile names them.

Build 1

Library 1

Runtime 1

Test 1

The full lists below include those, and their dependencies in turn.

Build dependencies 20
Run dependencies 16

Configuration

Options name: biology_bcftools

OptionDefaultDescription
GPLonEnable modules that rely on GPL code
PERLonEnable external PERL scripts for advanced filtering
USES
autoreconf gmake localbase perl5 python:env shebangfix
Service scripts
none

Message after installing

===>   NOTICE:

The bcftools port currently does not have a maintainer. As a result, it is
more likely to have unresolved issues, not be up-to-date, or even be removed in
the future. To volunteer to maintain this port, please create an issue at:

https://bugs.freebsd.org/bugzilla

More information about port maintainership is available at:

https://docs.freebsd.org/en/articles/contributing/#ports-contributing

Files

Manual pages 1
  • bcftools(1)
pkg-plist 53
  • bin/bcftools
  • bin/color-chrs
  • bin/gff2gff
  • bin/gff2gff.py
  • bin/guess-ploidy
  • bin/plot-roh
  • bin/plot-vcfstats
  • bin/roh-viz
  • bin/run-roh
  • bin/vcfutils
  • bin/vrfs-variances
  • libexec/bcftools/GTisec.so
  • libexec/bcftools/GTsubset.so
  • libexec/bcftools/ad-bias.so
  • libexec/bcftools/add-variantkey.so
  • libexec/bcftools/af-dist.so
  • libexec/bcftools/allele-length.so
  • libexec/bcftools/check-ploidy.so
  • libexec/bcftools/check-sparsity.so
  • libexec/bcftools/color-chrs.so
  • libexec/bcftools/contrast.so
  • libexec/bcftools/counts.so
  • libexec/bcftools/dosage.so
  • libexec/bcftools/fill-AN-AC.so
  • libexec/bcftools/fill-from-fasta.so
  • libexec/bcftools/fill-tags.so
  • libexec/bcftools/fixploidy.so
  • libexec/bcftools/fixref.so
  • libexec/bcftools/frameshifts.so
  • libexec/bcftools/guess-ploidy.so
  • libexec/bcftools/gvcfz.so
  • libexec/bcftools/impute-info.so
  • libexec/bcftools/indel-stats.so
  • libexec/bcftools/isecGT.so
  • libexec/bcftools/mendelian2.so
  • libexec/bcftools/missing2ref.so
  • libexec/bcftools/parental-origin.so
  • libexec/bcftools/prune.so
  • libexec/bcftools/remove-overlaps.so
  • libexec/bcftools/scatter.so
  • libexec/bcftools/setGT.so
  • libexec/bcftools/smpl-stats.so
  • libexec/bcftools/split-vep.so
  • libexec/bcftools/split.so
  • libexec/bcftools/tag2tag.so
  • libexec/bcftools/trio-dnm3.so
  • libexec/bcftools/trio-stats.so
  • libexec/bcftools/trio-switch-rate.so
  • libexec/bcftools/variant-distance.so
  • libexec/bcftools/variantkey-hex.so
  • libexec/bcftools/vcf2table.so
  • libexec/bcftools/vrfs.so
  • share/man/man1/bcftools.1.gz
distinfo 1
FileSizeSHA256
samtools-bcftools-1.24_GH0.tar.gz3.800098e+06386ac0d2fa51da312d01aada488ec98cf44ea4bac00d2a6c6d4993291b2f8e8c

Commit history 2

DateCommitCreditsLog message
2414383046 Jason W. Bacon Release numerous ports to ports@
I've been retired for a few years, and it is unlikely I will be doing any more scientific computing support in the future. I have continued to maintain ~160 ports to the best of my ability, mainly as a favor to the community, but I can no longer justify the time and effort required. I am therefore releasing most of my scientific ports, along with a few others, to ports@. I will continue to maintain ports I am actively using and those for which I am upstream.
c688db2d76 Jason W. Bacon biology/bcftools: Update to 1.24
Numerous fixes and enhancements Changes: https://github.com/samtools/bcftools/releases Reported by: portscout