non port: biology/htslib/Makefile |
Number of commits found: 24 |
Saturday, 27 Jan 2024
|
12:37 Muhammad Moinur Rahman (bofh)
biology/htslib: Moved man to share/man
Approved by: portmgr (blanket)
2eb9c98 |
Tuesday, 18 Apr 2023
|
21:55 Robert Clausecker (fuz)
biology/htslib: fix build on armv7
This project includes some SIMD-enhanced functions for ARM NEON.
Unfortunately the code uses a bunch of intrinsics only available on
aarch64. Disable the use of NEON on armv6 and armv7 to fix the build
on these platforms.
See also: https://github.com/samtools/htslib/issues/1603
Approved by: portmgr (build fix blanket)
bba4910 |
Friday, 24 Feb 2023
|
23:23 Jason W. Bacon (jwb)
biology/htslib: Update to 1.17
Numerous enhancements and fixes
Changes: https://github.com/samtools/htslib/releases
Reported by: portscout
5ce4151 |
Thursday, 5 Jan 2023
|
23:16 Jason W. Bacon (jwb)
biology/htslib: Update to 1.16
Numerous minor enhancements and bug fixes
Changes: https://github.com/samtools/htslib/releases
2d9e290 |
Wednesday, 7 Sep 2022
|
21:10 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.
This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.
There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.
The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.
Approved by: portmgr (tcberner)
b7f0544 |
Wednesday, 20 Jul 2022
|
14:20 Tobias C. Berner (tcberner)
biology: remove 'Created by' lines
A big Thank You to the original contributors of these ports:
* Aaron Dalton <aaron@FreeBSD.org>
* Akinori MUSHA aka knu <knu@idaemons.org>
* Andrey Zakhvatov
* Bob Zimmermann <rpz@cse.wustl.edu>
* Camson Huynh <chuynh@biolateral.com.au>
* Dan Siercks <dsiercks@uwm.edu>
* Fernan Aguero <fernan@iib.unsam.edu.ar>
* Hannes Hauswedell <h2+fbsdports@fsfe.org>
* J. Bacon <jwb@FreeBSD.org>
* Jason Bacon <jwb@FreeBSD.org>
* Jeremy <karlj000@unbc.ca>
* Johann Visagie <johann@egenetics.com>
* Johann Visagie <wjv@FreeBSD.org>
* Mauricio Herrera Cuadra <mauricio@arareko.net>
* Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
* Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
* Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
* Motomichi Matsuzaki <mzaki@niid.go.jp>
* Po-Chuan Hsieh <sunpoet@FreeBSD.org>
* Razi Khaja <razi@genet.sickkids.on.ca>
* Reed A. Cartwright <cartwright@asu.edu>
* Ryo MIYAMOTO
* Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
* Sangwoo Shim <sangwoos@gmail.com>
* Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org>
* Tassilo Philipp <tphilipp@potion-studios.com>
* Tony Maher
* Tony Maher <tonym@biolateral.com.au>
* Wen Heping <wen@FreeBSD.org>
* Wen Heping <wenheping@gmail.com>
* Yonatan <onatan@gmail.com>
* Yuri Victorovich <yuri@rawbw.com>
* ballen
* barnhart@genetics.wustl.edu
* camson@bilateral.com.au
* chuynh@biolateral.com.au
* dbader@eece.unm.edu
* frankch@waru.life.nthu.edu.tw
* h2
* lentferj
* maho@FreeBSD.org
* mzaki@biol.s.u-tokyo.ac.jp
* tonym
* wen@FreeBSD.org
With hat: portmgr
37526bb |
Saturday, 26 Feb 2022
|
15:04 Jason W. Bacon (jwb)
biology/htslib: Update to 1.15
A few minor bug fixes and enhancements
No API changes affecting existing dependents
Reported by: portscout
b3b13f5 |
Saturday, 18 Dec 2021
|
17:56 Jason W. Bacon (jwb)
biology/htslib: Update to 1.14
Several minor enhancements and fixes
Changes: https://github.com/samtools/htslib/tags
134a1c9 |
Friday, 10 Sep 2021
|
21:18 Bernhard Froehlich (decke)
biology/htslib: Add CPE information
Approved by: portmgr (blanket)
8522c83 |
Monday, 12 Jul 2021
|
13:16 Jason W. Bacon (jwb)
htslib: Update to 1.13
Numerous enhancements and bug fixes
Changes: https://github.com/samtools/htslib/releases/tag/1.13
5fa0712 |
Tuesday, 6 Apr 2021
|
14:31 Mathieu Arnold (mat)
Remove # $FreeBSD$ from Makefiles.
305f148 |
Saturday, 20 Mar 2021
|
17:14 jwb
biology/htslib: Update to 1.12
biology/samtools: Update to 1.12
biology/bcftools: Update to 1.12
Numerous enhancements, performance improvements, and bug fixes since 1.11
Build-tested all other htslib dependents, no revbumps should be needed
Reported by: portscout
|
Thursday, 5 Nov 2020
|
20:30 jwb
biology/htslib: Upgrade to 1.11.0
Numerous bug fixes, new features and performance improvements since 1.10
https://github.com/samtools/htslib/releases/tag/1.11
Reported by: portscout
|
Monday, 3 Aug 2020
|
17:40 jwb
biology/htslib: Upgrade to 1.10.2
Numerous bug fixes and enhancements since 1.9:
https://github.com/samtools/htslib/tags
Bump PORTREVISION on dependents that don't require additional patching
PR: 248089
|
Thursday, 2 Aug 2018
|
19:27 fernape
biology/htslib: update to 1.9
PR: 230170
Submitted by: ndowens.fbsd@yandex.com
Approved by: tcberner (mentor)
Differential Revision: https://reviews.freebsd.org/D16568
|
Monday, 16 Jul 2018
|
18:11 yuri
biology/htslib: Update 1.6 -> 1.8
Port changes:
* Use DISTVERSION
* Add USES=localbase instead of CPPFLAGS/LDFLAGS
* Move USES=ssl to CURL_USES=ssl
* Update WWW
PR: 228908
Approved by: maintainer's timeout (cartwright@asu.edu; 35 days)
|
Wednesday, 25 Oct 2017
|
10:19 pizzamig
biology/htslib biology/bcftools biology/samtools: Update to 1.6
PR: 223094
Submitted by: mzaki@niid.go.jp
Approved by: cartwright@asu.edu (maintainer)
Approved by: olivier (mentor)
Differential Revision: https://reviews.freebsd.org/D12768
|
Friday, 21 Oct 2016
|
15:21 mat
Use USES=pathfix where applicable.
PR: 213195
Submitted by: mat
Exp-run by: antoine
Sponsored by: Absolight
Differential Revision: https://reviews.freebsd.org/D8093
|
Thursday, 26 May 2016
|
20:28 pi
biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1
Changes:
https://sourceforge.net/p/samtools/mailman/message/35033807/
PR: 209653
Submitted by: cartwright@asu.edu (maintainer)
|
Friday, 1 Apr 2016
|
13:29 mat
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.
With hat: portmgr
Sponsored by: Absolight
|
Friday, 25 Dec 2015
|
01:31 junovitch
biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3
- Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require
version 1.3 of htslib.
- Add CURL option to htslib
- Add TEST_TARGET with perl and bash dependencies for testing
- Tidy up spacing and pkg-message's
PR: 205524
PR: 205525
PR: 205526
Submitted by: cartwright@asu.edu (maintainer)
|
Wednesday, 6 May 2015
|
15:16 mat
Update ports in the [bcd]* categories to not use GH_COMMIT.
With minor cleanups to make things simpler.
With hat: portmgr
Sponsored by: Absolight
|
Friday, 6 Mar 2015
|
12:45 robak
biology/htslib: update 1.1 -> 1.2.1
PR: 198291
Submitted by: Reed Cartwright <cartwright@asu.edu>
|
Sunday, 14 Dec 2014
|
22:35 pawel
HTSlib is an implementation of a unified C library for accessing common file
formats, such as SAM, CRAM, VCF, and BCF, used for high-throughput sequencing
data. It is the core library used by samtools and bcftools.
WWW: http://www.htslib.org/
PR: 195591
Submitted by: Reed A. Cartwright <cartwright@asu.edu>
|
Number of commits found: 24 |