non port: biology/samtools/Makefile |
Number of commits found: 23 |
Saturday, 2 Mar 2024
|
19:40 Nuno Teixeira (eduardo)
biology/samtools: Move man pages to share/man
Approved by: portmgr (blanket)
01064ce |
Friday, 24 Feb 2023
|
23:27 Jason W. Bacon (jwb)
biology/samtools: Update to 1.17
Numerous enhancements and bug fixes
Changes: https://github.com/samtools/samtools/releases
Reported by: portscout
1993bfc |
Thursday, 5 Jan 2023
|
23:17 Jason W. Bacon (jwb)
biology/samtools: Update to 1.16.1
New "reference" subcommand to extract CRAM features (1.16)
Numerous minor enhancements and bug fixes
Changes: https://github.com/samtools/samtools/releases
193567c |
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/samtools: Update to 1.15
Several small enhancements and a few bug fixes
Changes: https://github.com/samtools/samtools/releases
Reported by: portscout
822ec74 |
Saturday, 18 Dec 2021
|
17:56 Jason W. Bacon (jwb)
biology/samtools: Update to 1.14
Several enhancements and minor bug fixes
Changes: https://github.com/samtools/samtools/tags
d0228a8 |
Monday, 12 Jul 2021
|
13:24 Jason W. Bacon (jwb)
biology/samtools: Update to 1.13
Numerous enhancements and bug fixes
Changes: https://github.com/samtools/samtools/releases/tag/1.13
1c1b494 |
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
|
20:32 jwb
biology/samtools: Upgrade to 1.11
Numerous new features, bug fixes and performance enhancements
https://github.com/samtools/samtools/releases/tag/1.11
Reported by: portscout
|
Monday, 3 Aug 2020
|
18:22 jwb
biology/samtools: Upgrade to 1.10
Numerous bug fixes and enhancements:
https://github.com/samtools/samtools/releases/tag/1.10
Take maintainership per ports/248089
PR: ports/248089
|
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
|
19:28 fernape
biology/samtools: update to 1.9
PR: 230171
Submitted by: ndowens.fbsd@yandex.com
Approved by: tcberner (mentor)
Differential Revision: https://reviews.freebsd.org/D16569
|
Monday, 4 Dec 2017
|
15:27 mat
Add a USES=python:env, that will not add a dependency on Python.
It has the same effect than setting PYTHON_NO_DEPENDS, but in a more
compact way.
Sponsored by: Absolight
|
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
|
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
|
Monday, 1 Feb 2016
|
21:59 marino
biology/samtools: document ncurses requirement (USES+=ncurses)
approved by: infrastructure blanket
|
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
|
12:53 robak
biology/samtools: update 1.1 -> 1.2
PR: 198292
Submitted by: Reed Cartwright <cartwright@asu.edu>
|
Monday, 15 Dec 2014
|
21:59 pawel
Samtools implements various utilities for post-processing alignments in the
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.
WWW: http://www.htslib.org/
PR: 195592
Submitted by: Reed A. Cartwright <cartwright@asu.edu>
|
Number of commits found: 23 |