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Port details
vcftools Tools for working with VCF genomics files
0.1.16 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 0.1.16Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2016-02-26 17:08:07
Last Update: 2021-09-25 20:28:38
Commit Hash: 311f6fb
License: LGPL3
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
Expand this list (35 items)
Collapse this list.
  1. /usr/local/share/licenses/vcftools-0.1.16/catalog.mk
  2. /usr/local/share/licenses/vcftools-0.1.16/LICENSE
  3. /usr/local/share/licenses/vcftools-0.1.16/LGPL3
  4. bin/fill-aa
  5. bin/fill-an-ac
  6. bin/fill-fs
  7. bin/fill-ref-md5
  8. bin/vcf-annotate
  9. bin/vcf-compare
  10. bin/vcf-concat
  11. bin/vcf-consensus
  12. bin/vcf-contrast
  13. bin/vcf-convert
  14. bin/vcf-fix-newlines
  15. bin/vcf-fix-ploidy
  16. bin/vcf-indel-stats
  17. bin/vcf-isec
  18. bin/vcf-merge
  19. bin/vcf-phased-join
  20. bin/vcf-query
  21. bin/vcf-shuffle-cols
  22. bin/vcf-sort
  23. bin/vcf-stats
  24. bin/vcf-subset
  25. bin/vcf-to-tab
  26. bin/vcf-tstv
  27. bin/vcf-validator
  28. bin/vcftools
  29. lib/perl5/site_perl/FaSlice.pm
  30. lib/perl5/site_perl/Vcf.pm
  31. lib/perl5/site_perl/VcfStats.pm
  32. man/man1/vcftools.1.gz
  33. @owner
  34. @group
  35. @mode
Collapse this list.
Dependency lines:
  • vcftools>0:biology/vcftools
To install the port:
cd /usr/ports/biology/vcftools/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/vcftools
  • pkg install vcftools
PKGNAME: vcftools
Flavors: there is no flavor information for this port.
distinfo:
Packages (timestamps in pop-ups are UTC):
vcftools
ABIlatestquarterly
FreeBSD:11:aarch640.1.160.1.16
FreeBSD:11:amd640.1.160.1.16
FreeBSD:11:armv60.1.140.1.16
FreeBSD:11:i3860.1.160.1.16
FreeBSD:11:mips--
FreeBSD:11:mips640.1.140.1.16
FreeBSD:12:aarch640.1.160.1.16
FreeBSD:12:amd640.1.160.1.16
FreeBSD:12:armv60.1.160.1.16
FreeBSD:12:armv70.1.160.1.16
FreeBSD:12:i3860.1.160.1.16
FreeBSD:12:mips--
FreeBSD:12:mips640.1.160.1.16
FreeBSD:12:powerpc64-0.1.16
FreeBSD:13:aarch640.1.160.1.16
FreeBSD:13:amd640.1.160.1.16
FreeBSD:13:armv60.1.160.1.16
FreeBSD:13:armv70.1.160.1.16
FreeBSD:13:i3860.1.160.1.16
FreeBSD:13:mips--
FreeBSD:13:mips640.1.160.1.16
FreeBSD:13:powerpc640.1.160.1.16
FreeBSD:14:aarch640.1.16-
FreeBSD:14:amd640.1.16-
FreeBSD:14:armv60.1.16-
FreeBSD:14:armv70.1.16-
FreeBSD:14:i3860.1.16-
FreeBSD:14:mips--
FreeBSD:14:mips640.1.16-
FreeBSD:14:powerpc640.1.16-
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.3 : devel/gmake
  2. pkgconf>=1.3.0_1 : devel/pkgconf
  3. autoconf>=2.69 : devel/autoconf
  4. automake>=1.16.1 : devel/automake
  5. perl5>=5.32.r0<5.33 : lang/perl5.32
Runtime dependencies:
  1. perl5>=5.32.r0<5.33 : lang/perl5.32
This port is required by:
for Run
  1. biology/ddocent

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/vcftools/vcftools/tar.gz/v0.1.16?dummy=/
Collapse this list.

Number of commits found: 9

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
25 Sep 2021 20:28:38
 files touched by this commit commit hash:311f6fb1d3d05f50c8af921c9cc9e06e17550aeb  0.1.16
Bernhard Froehlich (decke) search for other commits by this committer
biology/vcftools: Add CPE information

Approved by:	portmgr (blanket)
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  0.1.16
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  0.1.16
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
04 Aug 2018 01:29:29
Original commit files touched by this commit Revision:476330  0.1.16
jwb search for other commits by this committer
biology/vcftools: Update to 0.1.16, a security release

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D16587
31 Jan 2018 01:07:08
Original commit files touched by this commit Revision:460452  0.1.15
jwb search for other commits by this committer
Multiple ports:
Change maintainer email bacon4000@gmail.com to jwb@FreeBSD.org
Remove Created by comments for same user

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D14128
27 Nov 2017 23:05:40
Original commit files touched by this commit Revision:455000  0.1.15
jwb search for other commits by this committer
biology/vcftools: Upgrade to latest release 0.1.15

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13276
03 Jan 2017 17:06:49
Original commit files touched by this commit Revision:430483  0.1.14
jbeich search for other commits by this committer
Assume "pkg-config zlib" works after 9.x reached EOL

Many ports passed ZLIB_CFLAGS="-I/usr/include" ZLIB_LIBS="-L/usr/lib -lz"
which is unsafe at least with lang/gcc* that override some system headers
and have newer libgcc_s.so that our old version in base may not be
forward-compatible with.
26 Nov 2016 10:09:54
Original commit files touched by this commit Revision:427136  0.1.14
mat search for other commits by this committer
Fixup USE_GITHUB usage.

It already sets DISTNAME to a very nice unique name, do not set it
yourself.

Sponsored by:	Absolight
26 Feb 2016 17:07:59
Original commit files touched by this commit Revision:409624  0.1.14
rakuco search for other commits by this committer
New port: biology/vcftools.

A set of tools written in Perl and C++ for working with VCF files, such as
those generated by the 1000 Genomes Project.

WWW: https://github.com/vcftools/vcftools

PR:		206926
Submitted by:	Jason Bacon <bacon4000@gmail.com>

Number of commits found: 9