non port: biology/bowtie2/Makefile |
Number of commits found: 35 |
Thursday, 18 Jan 2024
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23:20 Jason W. Bacon (jwb)
biology/bowtie2: Update to 2.5.3
A few bug fixes
Add option for faster indexing of small indexes
Reported by: portscout
6bb47af |
Wednesday, 18 Oct 2023
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12:26 Jason W. Bacon (jwb)
biology/bowtie2: Update to 2.5.2
A few bug fixes
Changes: https://github.com/BenLangmead/bowtie2/releases
Reported by: portscout
fee1d76 |
Saturday, 21 Jan 2023
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22:30 Jason W. Bacon (jwb)
biology/bowtie2: Update to 2.5.1
A few minor fixes and enhancements
Changes: https://github.com/BenLangmead/bowtie2/tags
Reported by: portscout
65ce3f1 |
Friday, 4 Nov 2022
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23:49 Jason W. Bacon (jwb)
biology/bowtie2: Update to 2.5.0
Performance improvements and minor improvements
Changes: https://github.com/BenLangmead/bowtie2/tags
Reported by: portscout
f2f8bd7 |
Wednesday, 7 Sep 2022
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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
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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 |
Friday, 21 Jan 2022
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14:33 Jason W. Bacon (jwb)
biology/bowtie2: Update to 2.4.5
A few bug fixes
Changes: https://github.com/BenLangmead/bowtie2/tags
Reported by: portscout
bfdda43 |
Monday, 24 May 2021
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16:35 Jason W. Bacon (jwb)
biology/bowtie2: Update to 2.4.4
Fix deadlock issue in multithreaded execution
Reported by: portscout
4521502 |
Monday, 17 May 2021
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23:40 Jason W. Bacon (jwb)
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*)
1effaac |
Sunday, 18 Apr 2021
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15:53 Jason W. Bacon (jwb)
biology/bowtie2: Add support for powerpc64le
PR: 255092
Submitted by: pkubaj
48ddc73 |
Wednesday, 14 Apr 2021
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10:08 Ganael LAPLANCHE (martymac)
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
9ee8484 |
Wednesday, 7 Apr 2021
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08:09 Mathieu Arnold (mat)
One more small cleanup, forgotten yesterday.
Reported by: lwhsu
cf118cc |
Tuesday, 6 Apr 2021
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14:31 Mathieu Arnold (mat)
Remove # $FreeBSD$ from Makefiles.
305f148 |
Friday, 19 Feb 2021
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15:14 martymac
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
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Saturday, 30 Jan 2021
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17:43 jwb
biology/bowtie2: Reverse switch to devel/onetbb
Mistakenly believed onetbb was already committed
PR: 252683
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17:39 jwb
biology/bowtie2: Switch to devel/onetbb
PR: 252683
Submitted by: martymac
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Saturday, 7 Nov 2020
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13:47 jwb
biology/bowtie2: Upgrade to 2.4.2
Minor bug fix release
Reported by: portscout
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Friday, 17 Jul 2020
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10:12 martymac
Update devel/tbb to 2020.3 and bump dependent ports' revisions
Changelog: https://github.com/oneapi-src/oneTBB/blob/v2020.3/CHANGES
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Wednesday, 1 Apr 2020
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14:14 martymac
Update devel/tbb to 2020.2 and bump dependent port's revisions
Changelog: https://github.com/oneapi-src/oneTBB/blob/tbb_2020/CHANGES
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Sunday, 1 Mar 2020
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16:01 jwb
biology/bowtie2: Upgrade to 2.4.1
Numerous bugfixes and enhancements
Enable experimental support for aarch64
Reported by: portscout
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Thursday, 26 Dec 2019
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16:25 martymac
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
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Wednesday, 25 Sep 2019
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10:03 martymac
Update devel/tbb to 2019.8 and bump dependent ports' revisions
Changelog: https://github.com/intel/tbb/blob/tbb_2019/CHANGES
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Wednesday, 24 Apr 2019
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17:41 jwb
biology/bowtie2: Clarify CPU-specificity
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Sunday, 21 Apr 2019
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15:23 jwb
biology/bowtie2: Upgrade to 2.3.5.1
Disable aarch64. Upstream support has changed and I lack the resources
to develop new patches.
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Friday, 29 Mar 2019
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22:13 linimon
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)
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Monday, 18 Mar 2019
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17:30 jwb
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)
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Thursday, 11 Oct 2018
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14:47 martymac
Update devel/tbb to version 2019.1 and bump dependent ports' revisions
Also, reintegrate HTML documentation that was removed in previous version.
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Thursday, 4 Oct 2018
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10:03 martymac
Update devel/tbb to version 2019 and bump dependent port's revisions
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Thursday, 30 Nov 2017
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02:59 jwb
biology/bowtie2: Upgrade to 2.3.3.1
Approved by: jrm (mentor)
Differential Revision: https://reviews.freebsd.org/D13300
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Sunday, 17 Sep 2017
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07:03 martymac
Update tbb to 2018 and bump dependent ports' revisions
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Tuesday, 7 Mar 2017
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12:44 martymac
Update devel/tbb to 2017.5
Also bring the following changes:
- Fetch distfiles from Github
- Bump dependent ports' PORTREVISIONs
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Monday, 27 Feb 2017
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14:08 jbeich
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)
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Tuesday, 20 Dec 2016
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17:01 jrm
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
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Friday, 13 May 2016
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20:12 pi
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)
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Wednesday, 23 Mar 2016
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11:22 rakuco
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>
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Number of commits found: 35 |