| non port: biology/diamond/Makefile |
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SVNWeb
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Number of commits found: 69 |
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Tue, 13 Apr 2021
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[ 00:55 jrm (Joseph Mingrone) ]  46fc7df
biology/diamond: Update to 2.0.9
https://github.com/bbuchfink/diamond/releases/tag/v2.0.9
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Wed, 7 Apr 2021
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[ 08:09 mat (Mathieu Arnold) ] cf118cc (Only the first 10 of 8873 ports in this commit are shown above.  )
One more small cleanup, forgotten yesterday.
Reported by: lwhsu
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Tue, 6 Apr 2021
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[ 14:31 mat (Mathieu Arnold) ] 305f148 (Only the first 10 of 29333 ports in this commit are shown above. )
Remove # $FreeBSD$ from Makefiles.
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Thu, 11 Mar 2021
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[ 12:41 jrm ]  
biology/diamond: Update to 2.0.8
https://github.com/bbuchfink/diamond/releases/tag/v2.0.8
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Wed, 17 Feb 2021
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[ 16:43 jrm ]
biology/diamond: Update to 2.0.7
https://github.com/bbuchfink/diamond/releases/tag/v2.0.7
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Sun, 20 Dec 2020
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[ 20:21 jrm ]
biology/diamond: Update to version 2.0.6
https://github.com/bbuchfink/diamond/releases/tag/v2.0.6
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Tue, 1 Dec 2020
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[ 22:27 jrm ]
biology/diamond: Update to version 2.0.5
https://github.com/bbuchfink/diamond/releases/tag/v2.0.5
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Sun, 30 Aug 2020
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[ 16:14 jrm ]
biology/diamond: Update to version 2.0.4
Upstream changes:
https://github.com/bbuchfink/diamond/releases/tag/v2.0.3
https://github.com/bbuchfink/diamond/releases/tag/v2.0.4
Port changes:
Remove a patch that was upstreamed:
https://github.com/bbuchfink/diamond/pull/378
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Fri, 7 Aug 2020
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[ 11:20 jrm ]
biology/diamond: Update to version 2.0.2
Upstream changes:
https://github.com/bbuchfink/diamond/releases/tag/v2.0.1
https://github.com/bbuchfink/diamond/releases/tag/v2.0.2
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Tue, 28 Jul 2020
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[ 02:39 jrm ]
biology/diamond: Update to version 2.0.0
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v2.0.0
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Fri, 3 Jul 2020
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[ 11:22 jrm ]
biology/diamond: Update to version 0.9.36
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.36
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Sat, 27 Jun 2020
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[ 16:26 jrm ]
biology/diamond: Update to version 0.9.35
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.35
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Fri, 12 Jun 2020
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[ 12:12 jrm ]
biology/diamond: Update to version 0.9.34
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.34
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Wed, 3 Jun 2020
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[ 21:44 jrm ]
biology/diamond: Update to version 0.9.33
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.33
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Fri, 24 Apr 2020
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[ 23:04 jrm ]
biology/diamond: Update to version 0.9.32
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.32
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Sat, 21 Mar 2020
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[ 22:11 jrm ]
biology/diamond: Update to version 0.9.31.2
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.31
Also include two additional commits that fix a build error.
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Mon, 3 Feb 2020
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[ 15:55 jrm ]
biology/diamond: Update to version 0.9.30
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.30
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Wed, 20 Nov 2019
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[ 17:14 jrm ]
biology/diamond: Update to v0.9.29
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.29
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Thu, 7 Nov 2019
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[ 14:12 jrm ]
biology/diamond: Update to version 0.9.28
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.28
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Sun, 3 Nov 2019
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[ 01:34 jrm ]
biology/diamond: Update to version 0.9.27 (plus one fix)
Since compiling from source no longer performs a native build, remove
-mtune=generic from CLFAGS when package building.
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.27
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Wed, 18 Sep 2019
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[ 18:45 jrm ]
biology/diamond: Update to version 0.9.26
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.26
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Sun, 4 Aug 2019
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[ 23:35 jrm ]
biology/diamond: Update to version 0.9.25
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.25
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Mon, 31 Dec 2018
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[ 19:00 jrm ]
biology/diamond: Update to version 0.9.24
Port changes: Tune for package building based on the author's
recommendation.
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.24
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Tue, 25 Dec 2018
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[ 20:25 tcberner ] (Only the first 10 of 1277 ports in this commit are shown above. )
Change cmake default behaviour to outsource.
Ports that build out of source now simply can use "USES=cmake"
instead of "USES=cmake:outsource". Ports that fail to build
out of source now need to specify "USES=cmake:insource".
I tried to only set insource where explictely needed.
PR: 232038
Exp-run by: antoine
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Mon, 17 Dec 2018
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[ 19:12 jrm ]
biology/diamond: Update to 0.9.23 plus fixes after release
Also:
- update license since upstream changed to GPLv3
- only build/package for amd64, since it is untested on other architectures
and currently does not build on i386
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.23
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Mon, 14 May 2018
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[ 17:17 jrm ]
biology/diamond: Update to version 0.9.22
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.22
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Fri, 20 Apr 2018
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[ 21:23 jrm ]
biology/diamond: Update to version 0.9.21
Upstream changes: https://github.com/bbuchfink/diamond/releases
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Sat, 17 Mar 2018
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[ 15:29 jrm ]
biology/diamond: Update to version 0.9.19
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.19
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Thu, 15 Mar 2018
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[ 02:28 jrm ]
biology/diamond: Update to version 0.9.18-49
Pull in commits after the 0.9.18 release for build fixes.
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.18
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Thu, 1 Feb 2018
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[ 19:20 jrm ]
biology/diamond: Update to version 0.9.17
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.17
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Wed, 13 Dec 2017
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[ 16:31 jrm ]
biology/diamond: Update to version 0.9.14
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.14
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Fri, 17 Nov 2017
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[ 20:11 jrm ]
biology/diamond: Update to version 0.9.13
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.13
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Wed, 8 Nov 2017
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[ 16:06 jrm ]
biology/diamond: Update to version 0.9.12
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.12
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Fri, 3 Nov 2017
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[ 03:45 jrm ]
biology/diamond: Update to 0.9.11
Upstream changes: https://github.com/bbuchfink/diamond/releases
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Tue, 15 Aug 2017
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[ 20:45 jrm ]
biology/diamond: Update to version 0.9.10
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.10
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Mon, 3 Jul 2017
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[ 19:12 jrm ]
biology/diamond: Update to version 0.9.9
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.9
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Fri, 16 Jun 2017
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[ 14:49 jrm ]
biology/diamond: Update to version 0.9.8
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Sat, 3 Jun 2017
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[ 12:32 jrm ]
biology/diamond: Update to version 0.9.4
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.4
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Mon, 29 May 2017
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[ 15:24 jrm ]
biology/diamond: Update to version 0.9.3
Upstream changes: https://github.com/bbuchfink/diamond/releases
Approved by: swills (mentor, implicit)
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Tue, 23 May 2017
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[ 11:03 jrm ]
biology/diamond: Update to version 0.9.1
Upstream changes: https://github.com/bbuchfink/diamond/releases
- License has changed to AGPLv3
Approved by: swills (mentor, implicit)
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Fri, 21 Apr 2017
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[ 14:46 jrm ]
biology/diamond: Update to version 0.8.38
- The base compilers meet all of Diamond's requirements, so remove
compiler:c++11-lang from USES definition.
- Upstream release notes:
https://github.com/bbuchfink/diamond/releases/tag/v0.8.38
Approved by: swills (mentor, implicit)
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Sun, 2 Apr 2017
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[ 10:55 jrm ]
biology/diamond: Update to version 0.8.37
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.8.37
Approved by: swills (mentor, implicit)
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Sat, 1 Apr 2017
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[ 15:23 gerald ] (Only the first 10 of 1118 ports in this commit are shown above. )
Bump PORTREVISIONs for ports depending on the canonical version of GCC and
lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some
circumstances such as versions of FreeBSD or platforms).
This includes ports
- with USE_GCC=yes or USE_GCC=any,
- with USES=fortran,
- using using Mk/bsd.octave.mk which in turn has USES=fortran, and
- with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang,
c++11-lang, c++0x, c11, or gcc-c++11-lib.
PR: 216707
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Sun, 12 Feb 2017
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[ 14:04 jrm ]
biology/diamond: Update to version 0.8.36.
Approved by: swills (mentor, implicit)
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Sun, 5 Feb 2017
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[ 22:23 jrm ]
biology/diamond: Update to version 0.8.35.
Version 0.8.35 fixes a compiler error on i386.
Approved by: swills (mentor, implicit)
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Mon, 23 Jan 2017
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[ 13:19 jrm ]
biology/diamond: Update to version 0.8.34.
Upstream changelog: https://github.com/bbuchfink/diamond/releases
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D9288
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Mon, 16 Jan 2017
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[ 13:38 jrm ]
biology/diamond: Update to version 0.8.32.
Upstream changes: https://github.com/bbuchfink/diamond/releases
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D9197
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Thu, 12 Jan 2017
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[ 23:23 jrm ]
biology/diamond: Update to version 0.8.31.
Upstream changelog:
- Added compositional score adjustments (option --comp-based-stats
(0,1)). This is a useful feature for filtering false positive hits and
is enabled by default.
- Removed --single-domain option and replaced by --max-hsps, to set the
maximum number of Hsps per query/subject pair, to be consistent with
BLAST. This option is set to 1 by default as getting more than 1 Hsp
per subject seems to be confusing users.
- Added option --no-self-hits to filter identical self-hits.
Approved by: AMDmi3 (mentor)
Differential Revision: https://reviews.freebsd.org/D9134
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Fri, 30 Dec 2016
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[ 16:27 jrm ]
biology/diamond: Update to version 0.8.30
Upstream changes:
- slightly improved sensitivity
- added option to report unaligned queries: --unal (0=no, 1=yes)
- pairwise, XML and SAM format will report unaligned queries by default
- added option to filter alignments by subject cover (--subject-cover)
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D9000
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Sun, 18 Dec 2016
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[ 13:52 jrm ]
biology/diamond: Update to version 0.8.29
Upstream change: fixed an issue that could cause a crash when using view on
incomplete DAA files
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8832
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Mon, 28 Nov 2016
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[ 15:18 jrm ]
biology/diamond: Update to version 0.8.28
Correct LICENSE and set LICENSE_FILE
Upstream changelog:
- support for gzip compressed files containing multiple gzip streams
- support for the BLAST pairwise format (option -f 0)
- slightly improved sensitivity
Approved by: AMDmi3 (mentor)
Differential Revision: https://reviews.freebsd.org/D8652
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Sun, 6 Nov 2016
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[ 05:42 jrm ]
biology/diamond: Update to version 0.8.26
Release notes: https://github.com/bbuchfink/diamond/releases/tag/v0.8.26
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8447
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Mon, 17 Oct 2016
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[ 14:17 jrm ]
biology/diamond: update to version 0.8.24
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8268
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Mon, 10 Oct 2016
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[ 04:33 jrm ]
biology/diamond: update to version 0.8.23
Upstream release notes:
Added option to change the genetic code used for translation of query in
blastx mode (option --query-gencode, see here for a list of possible values:
https://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi).
Approved by: AMDmi3 (mentor)
Differential Revision: https://reviews.freebsd.org/D8202
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Fri, 23 Sep 2016
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[ 21:42 jrm ] (Only the first 10 of 16 ports in this commit are shown above. )
Update email address to jrm@FreeBSD.org for ports that I maintain
Reviewed by: mat, swills (mentor)
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D7995
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Tue, 13 Sep 2016
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[ 17:50 amdmi3 ]
- Update to 0.8.22
PR: 212603
Submitted by: jrm@ftfl.ca (maintainer)
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Tue, 6 Sep 2016
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[ 06:34 wen ]
- Update to 0.8.20
PR: 212399
Submitted by: jrm@ftfl.ca(maintainer)
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Thu, 25 Aug 2016
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[ 18:49 pawel ]
Update to version 0.8.19
PR: 212145
Submitted by: Joseph Mingrone (maintainer)
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Sun, 14 Aug 2016
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[ 21:47 brd ]
Update biology/diamond to 0.8.18.
PR: 211845
Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer)
Approved by: bdrewery (implicit)
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Fri, 5 Aug 2016
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[ 21:24 pawel ]
Update to version 0.8.17
PR: 211582
Submitted by: Joseph Mingrone (maintainer)
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Sun, 24 Jul 2016
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[ 18:06 riggs ]
Update to upstream release 0.8.16
PR: 211335
Submitted by: jrm@ftfl.ca (maintainer)
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Thu, 14 Jul 2016
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[ 16:53 pawel ]
Trim excess tabs, no-op change
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[ 16:49 pawel ]
Update to version 0.8.14
PR: 211078
Submitted by: Joseph Mingrone (maintainer)
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Thu, 7 Jul 2016
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[ 15:46 amdmi3 ]
- Update to 0.8.11
PR: 210877
Submitted by: jrm@ftfl.ca (maintainer)
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Thu, 30 Jun 2016
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[ 01:37 junovitch ]
biology/diamond: update 0.8.6 -> 0.8.9
PR: 210710
Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer)
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Fri, 17 Jun 2016
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[ 19:53 rm ]
biology/diamond: update to 0.8.6
PR: 210345
Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer)
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Thu, 9 Jun 2016
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[ 01:39 matthew ]
Update to 0.8.5
PR: 209611
Submitted by: jrm@ftfl.ca (maintainer)
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Wed, 18 May 2016
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[ 16:22 antoine ]
Fix DEPENDS
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Fri, 6 May 2016
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[ 08:45 wen ]
DNA query sequences against a protein reference database (BLASTP and BLASTX
alignment mode). The speedup over BLAST is up to 20,000 on short reads at a
typical sensitivity of 90-99% relative to BLAST depending on the data and
settings.
WWW: http://ab.inf.uni-tuebingen.de/software/diamond/
PR: 208998
Submitted by: jrm@ftfl.ca
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Number of commits found: 69 |
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