BSD Ports

biology/bcf-score 1.20_3 FreeBSD

Bcftools plugins for GWAS-VCF summary statistics files

System
FreeBSD
Repository
FreeBSD ports
Maintainer
[email protected]
Last update
Commit
2414383046
License
MIT
Categories
biology
Package size
104.3 KiB, 304.0 KiB installed

Description

Score is a set of tools in the form of a bcftools plugin, for handling and converting summary statistics files following the GWAS-VCF specification.

In the other systems

SystemPortVersion
FreeBSDbiology/bcf-score1.20_3
NetBSDbiology/bcf-score1.20nb1
DragonFlybiology/bcf-score1.20_1
HardenedBSDbiology/bcf-score1.20_3
GhostBSDbiology/bcf-score1.20_3

Install

Binary package:

pkg install bcf-score

From the ports tree:

cd /usr/ports/biology/bcf-score/ && make install clean

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

RUN_DEPENDS=	bcf-score>0:biology/bcf-score

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:latest1.20_31.20_3--1.20_3
FreeBSD:14:quarterly1.20_31.20_3n/a-1.20_3
FreeBSD:15:latest1.20_31.20_3n/a-1.20_3
FreeBSD:15:quarterly1.20_31.20_3n/an/an/a
FreeBSD:16:latest1.20_31.20_3n/an/an/a
FreeBSD:16:quarterlyn/an/an/an/an/a

Dependencies

As this port's Makefile names them.

Build 1

Library 2

Runtime 2

Test 1

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

Build dependencies 31
Run dependencies 29

No port depends on this one.

Configuration

No options to configure.

USES
autoreconf gmake localbase perl5 python:env shebangfix
Service scripts
none

Message after installing

===>   NOTICE:

The bcf-score 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

pkg-plist 7
  • libexec/bcftools/blup.so
  • libexec/bcftools/liftover.so
  • libexec/bcftools/metal.so
  • libexec/bcftools/munge.so
  • libexec/bcftools/pgs.so
  • libexec/bcftools/score.so
  • share/bcf-score/assoc_plot.R
distinfo 2
FileSizeSHA256
score_1.20-20240505.tar.gz96852c2ac510f0a48e3d2e61d1a9e219e030b1268cdcf3bf987217bbd16740d962d41
samtools-bcftools-1.20-1.22_GH0.tar.gz3.751342e+061608e547daf7bd5ab7d52dea57019f57da3fdfb29bc26dece1e8d01a999a9a2d
Master sites 1
  • https://software.broadinstitute.org/software/score/

Commit history 1

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.