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non port: biology/samtools/Makefile

Number of commits found: 23

Saturday, 2 Mar 2024
19:40 Nuno Teixeira (eduardo) search for other commits by this committer
biology/samtools: Move man pages to share/man

Approved by:	portmgr (blanket)
commit hash: 01064ce0bda11469f31eaabb93e6c1eefa968661 commit hash: 01064ce0bda11469f31eaabb93e6c1eefa968661 commit hash: 01064ce0bda11469f31eaabb93e6c1eefa968661 commit hash: 01064ce0bda11469f31eaabb93e6c1eefa968661 01064ce
Friday, 24 Feb 2023
23:27 Jason W. Bacon (jwb) search for other commits by this committer
biology/samtools: Update to 1.17

Numerous enhancements and bug fixes

Changes: https://github.com/samtools/samtools/releases

Reported by:    portscout
commit hash: 1993bfc7cf7d933c1a8cc11bf2198ce8691a0d76 commit hash: 1993bfc7cf7d933c1a8cc11bf2198ce8691a0d76 commit hash: 1993bfc7cf7d933c1a8cc11bf2198ce8691a0d76 commit hash: 1993bfc7cf7d933c1a8cc11bf2198ce8691a0d76 1993bfc
Thursday, 5 Jan 2023
23:17 Jason W. Bacon (jwb) search for other commits by this committer
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
commit hash: 193567cc9e20e9ecb305506d92f522fc77dd18e4 commit hash: 193567cc9e20e9ecb305506d92f522fc77dd18e4 commit hash: 193567cc9e20e9ecb305506d92f522fc77dd18e4 commit hash: 193567cc9e20e9ecb305506d92f522fc77dd18e4 193567c
Wednesday, 7 Sep 2022
21:10 Stefan E├čer (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.

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)
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 b7f0544
Wednesday, 20 Jul 2022
14:20 Tobias C. Berner (tcberner) search for other commits by this committer
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
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 37526bb
Saturday, 26 Feb 2022
15:04 Jason W. Bacon (jwb) search for other commits by this committer
biology/samtools: Update to 1.15

Several small enhancements and a few bug fixes
Changes: https://github.com/samtools/samtools/releases

Reported by:    portscout
commit hash: 822ec7476b36d4a004c88067044432fbc29ca9f4 commit hash: 822ec7476b36d4a004c88067044432fbc29ca9f4 commit hash: 822ec7476b36d4a004c88067044432fbc29ca9f4 commit hash: 822ec7476b36d4a004c88067044432fbc29ca9f4 822ec74
Saturday, 18 Dec 2021
17:56 Jason W. Bacon (jwb) search for other commits by this committer
biology/samtools: Update to 1.14

Several enhancements and minor bug fixes

Changes: https://github.com/samtools/samtools/tags
commit hash: d0228a8a5f1c2b80211af892f32847ff4edb241f commit hash: d0228a8a5f1c2b80211af892f32847ff4edb241f commit hash: d0228a8a5f1c2b80211af892f32847ff4edb241f commit hash: d0228a8a5f1c2b80211af892f32847ff4edb241f d0228a8
Monday, 12 Jul 2021
13:24 Jason W. Bacon (jwb) search for other commits by this committer
biology/samtools: Update to 1.13

Numerous enhancements and bug fixes

Changes:        https://github.com/samtools/samtools/releases/tag/1.13
commit hash: 1c1b4943aef7525da9e15fb8f419c08e2f8849bf commit hash: 1c1b4943aef7525da9e15fb8f419c08e2f8849bf commit hash: 1c1b4943aef7525da9e15fb8f419c08e2f8849bf commit hash: 1c1b4943aef7525da9e15fb8f419c08e2f8849bf 1c1b494
Tuesday, 6 Apr 2021
14:31 Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb commit hash: 305f148f482daf30dcf728039d03d019f88344eb 305f148
Saturday, 20 Mar 2021
17:14 jwb search for other commits by this committer
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
Original commitRevision:568874 
Thursday, 5 Nov 2020
20:32 jwb search for other commits by this committer
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
Original commitRevision:554156 
Monday, 3 Aug 2020
18:22 jwb search for other commits by this committer
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
Original commitRevision:544098 
17:40 jwb search for other commits by this committer
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
Original commitRevision:544090 
Thursday, 2 Aug 2018
19:28 fernape search for other commits by this committer
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
Original commitRevision:476246 
Monday, 4 Dec 2017
15:27 mat search for other commits by this committer
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
Original commitRevision:455518 
Wednesday, 25 Oct 2017
10:19 pizzamig search for other commits by this committer
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
Original commitRevision:452840 
Thursday, 26 May 2016
20:28 pi search for other commits by this committer
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)
Original commitRevision:415914 
Friday, 1 Apr 2016
13:29 mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
Original commitRevision:412344 
Monday, 1 Feb 2016
21:59 marino search for other commits by this committer
biology/samtools: document ncurses requirement (USES+=ncurses)

approved by:	infrastructure blanket
Original commitRevision:407776 
Friday, 25 Dec 2015
01:31 junovitch search for other commits by this committer
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)
Original commitRevision:404398 
Wednesday, 6 May 2015
15:16 mat search for other commits by this committer
Update ports in the [bcd]* categories to not use GH_COMMIT.

With minor cleanups to make things simpler.

With hat:	portmgr
Sponsored by:	Absolight
Original commitRevision:385521 
Friday, 6 Mar 2015
12:53 robak search for other commits by this committer
biology/samtools: update 1.1 -> 1.2

PR:		198292
Submitted by:	Reed Cartwright <cartwright@asu.edu>
Original commitRevision:380597 
Monday, 15 Dec 2014
21:59 pawel search for other commits by this committer
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>
Original commitRevision:374767 

Number of commits found: 23