non port: biology/diamond/distinfo |
Number of commits found: 75 |
Sunday, 4 Feb 2024
|
19:41 Joseph Mingrone (jrm)
biology/diamond: Update to 2.1.9
Changelog: https://github.com/bbuchfink/diamond/releases/tag/v2.1.9
Sponsored by: The FreeBSD Foundation
92b051a |
Saturday, 8 Jul 2023
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03:45 Joseph Mingrone (jrm)
biology/diamond: Update to 2.1.8
Changes: https://github.com/bbuchfink/diamond/releases/tag/v2.1.7
https://github.com/bbuchfink/diamond/releases/tag/v2.1.8
Sponsored by: The FreeBSD Foundation
371eba1 |
Saturday, 18 Mar 2023
|
15:49 Joseph Mingrone (jrm)
biology/diamond: Update to 2.1.6
Changes: https://github.com/bbuchfink/diamond/releases/tag/v2.1.5
https://github.com/bbuchfink/diamond/releases/tag/v2.1.6
Sponsored by: The FreeBSD Foundation
43743a8 |
Sunday, 5 Mar 2023
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15:33 Joseph Mingrone (jrm)
biology/diamond: Update to 2.1.4
Changes: https://github.com/bbuchfink/diamond/releases/tag/v2.1.4
Sponsored by: The FreeBSD Foundation
d363e4b |
Wednesday, 22 Feb 2023
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11:48 Joseph Mingrone (jrm)
biology/diamond: Update to 2.1.3
Changes: https://github.com/bbuchfink/diamond/releases/tag/v2.1.3
Sponsored by: The FreeBSD Foundation
85920ea |
Monday, 20 Feb 2023
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14:35 Joseph Mingrone (jrm)
biology/diamond: Update to 2.1.2
Changes: https://github.com/bbuchfink/diamond/releases/tag/v2.1.2
Sponsored by: The FreeBSD Foundation
89f956f |
Friday, 10 Feb 2023
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17:36 Joseph Mingrone (jrm)
biology/diamond: Update to 2.1.1
Changes: https://github.com/bbuchfink/diamond/releases/tag/v2.1.0
https://github.com/bbuchfink/diamond/releases/tag/v2.1.1
Sponsored by: The FreeBSD Foundation
0562554 |
Sunday, 24 Apr 2022
|
17:50 Joseph Mingrone (jrm)
biology/diamond: Update to 2.0.15
https://github.com/bbuchfink/diamond/releases/tag/v2.0.15
Sponsored by: The FreeBSD Foundation
d9f5d5d |
Thursday, 13 Jan 2022
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17:42 Joseph Mingrone (jrm)
biology/diamond: Update to 2.0.14
https://github.com/bbuchfink/diamond/releases/tag/v2.0.14
Sponsored by: The FreeBSD Foundation
7c428e8 |
Thursday, 11 Nov 2021
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17:17 Joseph Mingrone (jrm)
biology/diamond: Update to 2.0.13
This update fixes a bug that caused invalid bit scores in frameshift
alignment mode.
84e457e |
Tuesday, 12 Oct 2021
|
15:40 Joseph Mingrone (jrm)
biology/diamond: Update to 2.0.12
https://github.com/bbuchfink/diamond/releases/tag/v2.0.12
523d253 |
Tuesday, 6 Jul 2021
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13:15 Joseph Mingrone (jrm)
biology/diamond: Update to 2.0.11-1
Includes a build fix for 2.0.11 on FreeBSD
https://github.com/bbuchfink/diamond/releases/tag/v2.0.11
d0bf21b |
Saturday, 3 Jul 2021
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16:25 Joseph Mingrone (jrm)
biology/diamond: Update to 2.0.10
https://github.com/bbuchfink/diamond/releases/tag/v2.0.10
4335856 |
Tuesday, 13 Apr 2021
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00:55 Joseph Mingrone (jrm)
biology/diamond: Update to 2.0.9
https://github.com/bbuchfink/diamond/releases/tag/v2.0.9
46fc7df |
Thursday, 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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Wednesday, 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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Sunday, 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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Tuesday, 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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Sunday, 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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Friday, 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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Tuesday, 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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Friday, 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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Saturday, 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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Friday, 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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Wednesday, 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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Friday, 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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Saturday, 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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Monday, 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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Wednesday, 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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Thursday, 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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Sunday, 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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Wednesday, 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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Sunday, 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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Monday, 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
|
Monday, 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
|
Monday, 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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Friday, 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
|
Saturday, 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
|
Thursday, 15 Mar 2018
|
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
|
Thursday, 1 Feb 2018
|
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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Wednesday, 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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Friday, 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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Wednesday, 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
|
Friday, 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
|
Tuesday, 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
|
Monday, 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
|
Friday, 16 Jun 2017
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14:49 jrm
biology/diamond: Update to version 0.9.8
|
Saturday, 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
|
Monday, 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)
|
Tuesday, 23 May 2017
|
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)
|
Friday, 21 Apr 2017
|
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)
|
Sunday, 2 Apr 2017
|
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)
|
Sunday, 12 Feb 2017
|
14:04 jrm
biology/diamond: Update to version 0.8.36.
Approved by: swills (mentor, implicit)
|
Sunday, 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)
|
Monday, 23 Jan 2017
|
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
|
Monday, 16 Jan 2017
|
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
|
Thursday, 12 Jan 2017
|
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
|
Friday, 30 Dec 2016
|
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
|
Sunday, 18 Dec 2016
|
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
|
Monday, 28 Nov 2016
|
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
|
Sunday, 6 Nov 2016
|
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
|
Monday, 17 Oct 2016
|
14:17 jrm
biology/diamond: update to version 0.8.24
Approved by: swills (mentor)
Differential Revision: https://reviews.freebsd.org/D8268
|
Monday, 10 Oct 2016
|
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
|
Tuesday, 13 Sep 2016
|
17:50 amdmi3
- Update to 0.8.22
PR: 212603
Submitted by: jrm@ftfl.ca (maintainer)
|
Tuesday, 6 Sep 2016
|
06:34 wen
- Update to 0.8.20
PR: 212399
Submitted by: jrm@ftfl.ca(maintainer)
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Thursday, 25 Aug 2016
|
18:49 pawel
Update to version 0.8.19
PR: 212145
Submitted by: Joseph Mingrone (maintainer)
|
Sunday, 14 Aug 2016
|
21:47 brd
Update biology/diamond to 0.8.18.
PR: 211845
Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer)
Approved by: bdrewery (implicit)
|
Friday, 5 Aug 2016
|
21:24 pawel
Update to version 0.8.17
PR: 211582
Submitted by: Joseph Mingrone (maintainer)
|
Sunday, 24 Jul 2016
|
18:06 riggs
Update to upstream release 0.8.16
PR: 211335
Submitted by: jrm@ftfl.ca (maintainer)
|
Thursday, 14 Jul 2016
|
16:49 pawel
Update to version 0.8.14
PR: 211078
Submitted by: Joseph Mingrone (maintainer)
|
Thursday, 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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Thursday, 30 Jun 2016
|
01:37 junovitch
biology/diamond: update 0.8.6 -> 0.8.9
PR: 210710
Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer)
|
Friday, 17 Jun 2016
|
19:53 rm
biology/diamond: update to 0.8.6
PR: 210345
Submitted by: Joseph Mingrone <jrm@ftfl.ca> (maintainer)
|
Thursday, 9 Jun 2016
|
01:39 matthew
Update to 0.8.5
PR: 209611
Submitted by: jrm@ftfl.ca (maintainer)
|
Friday, 6 May 2016
|
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
|
Number of commits found: 75 |