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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 Version 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: 2022-09-07 21:58:51
Commit Hash: fb16dfe
License: LGPL3
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
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
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
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:mipspkg-falloutpkg-fallout
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:mipspkg-falloutpkg-fallout
FreeBSD:12:mips640.1.160.1.16
FreeBSD:12:powerpc64pkg-fallout0.1.16
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:mipspkg-falloutpkg-fallout
FreeBSD:13:mips640.1.160.1.16
FreeBSD:13:powerpc640.1.160.1.16
FreeBSD:13:riscv64pkg-fallout0.1.16
FreeBSD:14:aarch640.1.16pkg-fallout
FreeBSD:14:amd640.1.16pkg-fallout
FreeBSD:14:armv60.1.16pkg-fallout
FreeBSD:14:armv70.1.16pkg-fallout
FreeBSD:14:i3860.1.16pkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips640.1.16pkg-fallout
FreeBSD:14:powerpc640.1.16pkg-fallout
FreeBSD:14:riscv640.1.16pkg-fallout
 

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>=2.71 : devel/autoconf
  4. automake>=1.16.5 : 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: 11

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
07 Sep 2022 21:58:51
commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
0.1.16
07 Sep 2022 21:10:59
commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
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.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
0.1.16
25 Sep 2021 20:28:38
commit hash:311f6fb1d3d05f50c8af921c9cc9e06e17550aebcommit hash:311f6fb1d3d05f50c8af921c9cc9e06e17550aebcommit hash:311f6fb1d3d05f50c8af921c9cc9e06e17550aebcommit hash:311f6fb1d3d05f50c8af921c9cc9e06e17550aeb files touched by this commit
Bernhard Froehlich (decke) search for other commits by this committer
biology/vcftools: Add CPE information

Approved by:	portmgr (blanket)
0.1.16
07 Apr 2021 08:09:01
commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
0.1.16
06 Apr 2021 14:31:07
commit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
0.1.16
04 Aug 2018 01:29:29
Revision:476330Original commit files touched by this commit
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
0.1.15
31 Jan 2018 01:07:08
Revision:460452Original commit files touched by this commit
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
0.1.15
27 Nov 2017 23:05:40
Revision:455000Original commit files touched by this commit
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
0.1.14
03 Jan 2017 17:06:49
Revision:430483Original commit files touched by this commit
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.
0.1.14
26 Nov 2016 10:09:54
Revision:427136Original commit files touched by this commit
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
0.1.14
26 Feb 2016 17:07:59
Revision:409624Original commit files touched by this commit
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: 11