| Port details |
- vcftools Tools for working with VCF genomics files
- 0.1.16_2 biology
 =2      0.1.16_2Version of this port present on the latest quarterly branch. - Maintainer: jwb@FreeBSD.org
- Port Added: 2016-02-26 17:08:07
- Last Update: 2024-03-02 20:35:56
- Commit Hash: ebba67d
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: LGPL3
- WWW:
- https://github.com/vcftools/vcftools
- Description:
- A set of tools written in Perl and C++ for working with VCF files, such as
those generated by the 1000 Genomes Project.
  ¦  ¦  ¦  ¦ 
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - 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:
- TIMESTAMP = 1533330712
SHA256 (vcftools-vcftools-v0.1.16_GH0.tar.gz) = 575c13073efe65cbff6e2ab99eef12fe04536f5dc1f98de6674c848ca83cf302
SIZE (vcftools-vcftools-v0.1.16_GH0.tar.gz) = 246933
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- gmake>=4.3 : devel/gmake
- pkgconf>=1.3.0_1 : devel/pkgconf
- autoconf>=2.71 : devel/autoconf
- automake>=1.16.5 : devel/automake
- perl5>=5.36<5.37 : lang/perl5.36
- Runtime dependencies:
-
- perl5>=5.36<5.37 : lang/perl5.36
- This port is required by:
- for Run
-
- biology/ddocent
Configuration Options:- No options to configure
- Options name:
- biology_vcftools
- USES:
- autoreconf cpe gmake perl5 pkgconfig
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
0.1.16_2
02 Mar 2024 20:35:56
 |
Nuno Teixeira (eduardo) |
biology/vcftools: Move man pages to share/man
Approved by: portmgr (blanket) |
0.1.16_1
16 Jul 2023 01:29:00
|
Jason W. Bacon (jwb) |
biology/vcftools: Unbreak build with clang 16
Add -std=c++14
Reported by: pkg-fallout |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
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
|
Stefan Eßer (se) |
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  ) |
0.1.16
25 Sep 2021 20:28:38
|
Bernhard Froehlich (decke) |
biology/vcftools: Add CPE information
Approved by: portmgr (blanket) |
0.1.16
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
0.1.16
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.1.16
04 Aug 2018 01:29:29
 |
jwb |
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
|
jwb |
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
|
jwb |
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
|
jbeich |
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
|
mat |
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
|
rakuco |
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> |
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