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non port: biology/bowtie2/Makefile

Number of commits found: 35

Thursday, 18 Jan 2024
23:20 Jason W. Bacon (jwb) search for other commits by this committer
biology/bowtie2: Update to 2.5.3

A few bug fixes
Add option for faster indexing of small indexes

Reported by:    portscout
commit hash: 6bb47afdcc76e781b91e516bc1ceedd146447d24 commit hash: 6bb47afdcc76e781b91e516bc1ceedd146447d24 commit hash: 6bb47afdcc76e781b91e516bc1ceedd146447d24 commit hash: 6bb47afdcc76e781b91e516bc1ceedd146447d24 6bb47af
Wednesday, 18 Oct 2023
12:26 Jason W. Bacon (jwb) search for other commits by this committer
biology/bowtie2: Update to 2.5.2

A few bug fixes
Changes: https://github.com/BenLangmead/bowtie2/releases

Reported by:    portscout
commit hash: fee1d76936f6a36a27b271d0dbe7685b4fd84cc0 commit hash: fee1d76936f6a36a27b271d0dbe7685b4fd84cc0 commit hash: fee1d76936f6a36a27b271d0dbe7685b4fd84cc0 commit hash: fee1d76936f6a36a27b271d0dbe7685b4fd84cc0 fee1d76
Saturday, 21 Jan 2023
22:30 Jason W. Bacon (jwb) search for other commits by this committer
biology/bowtie2: Update to 2.5.1

A few minor fixes and enhancements

Changes:    https://github.com/BenLangmead/bowtie2/tags

Reported by:    portscout
commit hash: 65ce3f1684bc6a0457bfc55feb059baf76bbee2a commit hash: 65ce3f1684bc6a0457bfc55feb059baf76bbee2a commit hash: 65ce3f1684bc6a0457bfc55feb059baf76bbee2a commit hash: 65ce3f1684bc6a0457bfc55feb059baf76bbee2a 65ce3f1
Friday, 4 Nov 2022
23:49 Jason W. Bacon (jwb) search for other commits by this committer
biology/bowtie2: Update to 2.5.0

Performance improvements and minor improvements
Changes:    https://github.com/BenLangmead/bowtie2/tags

Reported by:    portscout
commit hash: f2f8bd75c4acf8a9c1fb5d51a0f381e25a9006fa commit hash: f2f8bd75c4acf8a9c1fb5d51a0f381e25a9006fa commit hash: f2f8bd75c4acf8a9c1fb5d51a0f381e25a9006fa commit hash: f2f8bd75c4acf8a9c1fb5d51a0f381e25a9006fa f2f8bd7
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
Friday, 21 Jan 2022
14:33 Jason W. Bacon (jwb) search for other commits by this committer
biology/bowtie2: Update to 2.4.5

A few bug fixes

Changes:        https://github.com/BenLangmead/bowtie2/tags
Reported by:    portscout
commit hash: bfdda4387466c93127ca47424f61e03c94aae8bb commit hash: bfdda4387466c93127ca47424f61e03c94aae8bb commit hash: bfdda4387466c93127ca47424f61e03c94aae8bb commit hash: bfdda4387466c93127ca47424f61e03c94aae8bb bfdda43
Monday, 24 May 2021
16:35 Jason W. Bacon (jwb) search for other commits by this committer
biology/bowtie2: Update to 2.4.4

Fix deadlock issue in multithreaded execution

Reported by:    portscout
commit hash: 4521502b9bd34932d3547b69cd5aea3c221fad88 commit hash: 4521502b9bd34932d3547b69cd5aea3c221fad88 commit hash: 4521502b9bd34932d3547b69cd5aea3c221fad88 commit hash: 4521502b9bd34932d3547b69cd5aea3c221fad88 4521502
Monday, 17 May 2021
23:40 Jason W. Bacon (jwb) search for other commits by this committer
biology/bowtie2: Update to 2.4.3

Drop tbb dependency (upstream switched to C++ threads)
Add support for powerpc64

Reported by:    portscout
Tested by:      pkubaj (powerpc64*)
commit hash: 1effaacbafd70e1bcf3e544d6a7b49bad3ca88ef commit hash: 1effaacbafd70e1bcf3e544d6a7b49bad3ca88ef commit hash: 1effaacbafd70e1bcf3e544d6a7b49bad3ca88ef commit hash: 1effaacbafd70e1bcf3e544d6a7b49bad3ca88ef 1effaac
Sunday, 18 Apr 2021
15:53 Jason W. Bacon (jwb) search for other commits by this committer
biology/bowtie2: Add support for powerpc64le

PR:             255092
Submitted by:   pkubaj
commit hash: 48ddc73c5822130dd3f00361ec6998eec0a29e6d commit hash: 48ddc73c5822130dd3f00361ec6998eec0a29e6d commit hash: 48ddc73c5822130dd3f00361ec6998eec0a29e6d commit hash: 48ddc73c5822130dd3f00361ec6998eec0a29e6d 48ddc73
Wednesday, 14 Apr 2021
10:08 Ganael LAPLANCHE (martymac) search for other commits by this committer
devel/onetbb: Update to 2021.2.0 and bump dependencies

Changelog:
https://software.intel.com/content/www/us/en/develop/articles/intel-oneapi-threading-building-blocks-release-notes.html
commit hash: 9ee84848094757a07a41aefc97967e6ae1a43039 commit hash: 9ee84848094757a07a41aefc97967e6ae1a43039 commit hash: 9ee84848094757a07a41aefc97967e6ae1a43039 commit hash: 9ee84848094757a07a41aefc97967e6ae1a43039 9ee8484
Wednesday, 7 Apr 2021
08:09 Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c cf118cc
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
Friday, 19 Feb 2021
15:14 martymac search for other commits by this committer
Introduce devel/onetbb and mark devel/tbb as legacy

Intel oneAPI tbb 2021.1 (onetbb) has been released[1][2] and has deprecated
several interfaces over tbb 2020, breaking most dependent ports.

Old tbb 2020 will be kept for a certain time to allow transition but will be
removed in a near future as it CONFLICTS with devel/onetbb. New ports should
now use devel/onetbb instead of devel/tbb.

We tried to move a maximum number of dependent ports to devel/onetbb (or
disable dependency when not possible), but some of them still remain stuck
to devel/tbb. Remaining ones have not been identified as major dependencies
themselves and will be fixed as soon as updates are available from upstream.

PR:		252648, 252688 [3], 252683 [4], 252651 [5], 252690 [3], 252693 [3],
	252695 [3], 252696 [3], 252786 [3], 252649, 252868 [6], 252870 [5],
	252684 [7], 252785 [7]
Approved by:	yuri [3], jwb [4], thierry [5], FreeBSD@Shaneware.biz [6],
	maintainer timeout [7]

[1]
https://software.intel.com/content/www/us/en/develop/articles/intel-oneapi-threading-building-blocks-release-notes.html
[2]
https://software.intel.com/content/www/us/en/develop/articles/tbb-revamp.html
Original commitRevision:566074 
Saturday, 30 Jan 2021
17:43 jwb search for other commits by this committer
biology/bowtie2: Reverse switch to devel/onetbb

Mistakenly believed onetbb was already committed

PR:             252683
Original commitRevision:563428 
17:39 jwb search for other commits by this committer
biology/bowtie2: Switch to devel/onetbb

PR:             252683
Submitted by:   martymac
Original commitRevision:563427 
Saturday, 7 Nov 2020
13:47 jwb search for other commits by this committer
biology/bowtie2: Upgrade to 2.4.2

Minor bug fix release

Reported by:    portscout
Original commitRevision:554390 
Friday, 17 Jul 2020
10:12 martymac search for other commits by this committer
Update devel/tbb to 2020.3 and bump dependent ports' revisions

Changelog: https://github.com/oneapi-src/oneTBB/blob/v2020.3/CHANGES
Original commitRevision:542423 
Wednesday, 1 Apr 2020
14:14 martymac search for other commits by this committer
Update devel/tbb to 2020.2 and bump dependent port's revisions

Changelog: https://github.com/oneapi-src/oneTBB/blob/tbb_2020/CHANGES
Original commitRevision:530219 
Sunday, 1 Mar 2020
16:01 jwb search for other commits by this committer
biology/bowtie2: Upgrade to 2.4.1

Numerous bugfixes and enhancements
Enable experimental support for aarch64

Reported by:    portscout
Original commitRevision:527560 
Thursday, 26 Dec 2019
16:25 martymac search for other commits by this committer
Update devel/tbb to 2020.0 and bump dependent ports' revisions [1]

Also, while here, re-generate patches using the makepatch target

[1] Changelog: https://github.com/intel/tbb/blob/v2020.0/CHANGES
Original commitRevision:520935 
Wednesday, 25 Sep 2019
10:03 martymac search for other commits by this committer
Update devel/tbb to 2019.8 and bump dependent ports' revisions

Changelog: https://github.com/intel/tbb/blob/tbb_2019/CHANGES
Original commitRevision:512777 
Wednesday, 24 Apr 2019
17:41 jwb search for other commits by this committer
biology/bowtie2: Clarify CPU-specificity
Original commitRevision:499873 
Sunday, 21 Apr 2019
15:23 jwb search for other commits by this committer
biology/bowtie2: Upgrade to 2.3.5.1

Disable aarch64.  Upstream support has changed and I lack the resources
to develop new patches.
Original commitRevision:499544 
Friday, 29 Mar 2019
22:13 linimon search for other commits by this committer
Mark as broken on aarch64:

  usage: dirname string [...]

My guess is that some parameter is being passed the empty string.

Approved by:	portmgr (tier-2 blanket)
Original commitRevision:497212 
Monday, 18 Mar 2019
17:30 jwb search for other commits by this committer
biology/bowtie2: Upgrade to 2.3.5

-   Add bowtie2-test script
-   Separate Makefile patches into a static patch for upstream and reinplace
    for ports-specifics
-   Allow aarch64 per upstream Makefile (untested)
Original commitRevision:496155 
Thursday, 11 Oct 2018
14:47 martymac search for other commits by this committer
Update devel/tbb to version 2019.1 and bump dependent ports' revisions

Also, reintegrate HTML documentation that was removed in previous version.
Original commitRevision:481833 
Thursday, 4 Oct 2018
10:03 martymac search for other commits by this committer
Update devel/tbb to version 2019 and bump dependent port's revisions
Original commitRevision:481215 
Thursday, 30 Nov 2017
02:59 jwb search for other commits by this committer
biology/bowtie2: Upgrade to 2.3.3.1

Approved by: jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D13300
Original commitRevision:455161 
Sunday, 17 Sep 2017
07:03 martymac search for other commits by this committer
Update tbb to 2018 and bump dependent ports' revisions
Original commitRevision:449986 
Tuesday, 7 Mar 2017
12:44 martymac search for other commits by this committer
Update devel/tbb to 2017.5

Also bring the following changes:
- Fetch distfiles from Github
- Bump dependent ports' PORTREVISIONs
Original commitRevision:435599 
Monday, 27 Feb 2017
14:08 jbeich search for other commits by this committer
biology/bowtie2: update to 2.3.0

- Unbreak with Clang 4.0

Changes:	https://github.com/BenLangmead/bowtie2/releases/tag/v2.3.0
PR:		216619
Submitted by:	Jason Bacon <bacon4000@gmail.com> (maintainer)
Original commitRevision:434940 
Tuesday, 20 Dec 2016
17:01 jrm search for other commits by this committer
biology/bowtie2: Update to version 2.2.9

- Update license information.
- Add python to USES (bowtie2-build bowtie2-inspect need python)
- Add DOCS and EXAMPLES options

Approved by:	AMDmi3 (mentor) swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8182
Original commitRevision:429003 
Friday, 13 May 2016
20:12 pi search for other commits by this committer
biology/bowtie2: 2.2.7 -> 2.2.8

- Various website updates
- Fixed the bowtie2-build issue that made TBB compilation fail

PR:		208943
Submitted by:	Joseph Mingrone <jrm@ftfl.ca>
Approved by:	Jason Bacon <bacon4000@gmail.com> (maintainer)
Original commitRevision:415148 
Wednesday, 23 Mar 2016
11:22 rakuco search for other commits by this committer
New port: biology/bowtie2.

Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short
DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp
reads per hour.

This is Bowtie version 2, which will need to coexists with Bowtie 1 for the
foreseeable future. Both are required by certain genomics pipelines, in some
cases (e.g. Trinity) by the same pipeline.

WWW: https://github.com/BenLangmead/bowtie2

PR:		207908
Submitted by:	Jason Bacon <bacon4000@gmail.com>
Original commitRevision:411698 

Number of commits found: 35