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70 Commits

Author SHA1 Message Date
Joseph Mingrone
46fc7df854
biology/diamond: Update to 2.0.9 
https://github.com/bbuchfink/diamond/releases/tag/v2.0.9
 2021-04-12 21:55:49 -03:00
Mathieu Arnold
cf118ccf87
One more small cleanup, forgotten yesterday. 
Reported by:	lwhsu
 2021-04-07 10:09:01 +02:00
Mathieu Arnold
305f148f48
Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
Joseph Mingrone
59815b0604 biology/diamond: Update to 2.0.8 
https://github.com/bbuchfink/diamond/releases/tag/v2.0.8
 2021-03-11 12:41:20 +00:00
Joseph Mingrone
93cbba555f biology/diamond: Update to 2.0.7 
https://github.com/bbuchfink/diamond/releases/tag/v2.0.7
 2021-02-17 16:43:27 +00:00
Joseph Mingrone
8d1a5bb642 biology/diamond: Update to version 2.0.6 
https://github.com/bbuchfink/diamond/releases/tag/v2.0.6
 2020-12-20 20:21:41 +00:00
Joseph Mingrone
273b0bb5c1 biology/diamond: Update to version 2.0.5 
https://github.com/bbuchfink/diamond/releases/tag/v2.0.5
 2020-12-01 22:27:24 +00:00
Joseph Mingrone
bc66849a97 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
 2020-08-30 16:14:22 +00:00
Joseph Mingrone
c565364c26 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
 2020-08-07 11:20:11 +00:00
Joseph Mingrone
32248779ba biology/diamond: Update to version 2.0.0 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v2.0.0
 2020-07-28 02:39:00 +00:00
Joseph Mingrone
5848822bf5 biology/diamond: Update to version 0.9.36 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.36
 2020-07-03 11:22:49 +00:00
Joseph Mingrone
bca3b9c7c6 biology/diamond: Update to version 0.9.35 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.35
 2020-06-27 16:26:54 +00:00
Joseph Mingrone
f177208d8a biology/diamond: Update to version 0.9.34 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.34
 2020-06-12 12:12:12 +00:00
Joseph Mingrone
1337e0f38e biology/diamond: Update to version 0.9.33 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.33
 2020-06-03 21:44:36 +00:00
Joseph Mingrone
0c4bc2a086 biology/diamond: Update to version 0.9.32 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.32
 2020-04-24 23:04:14 +00:00
Joseph Mingrone
0ca170c44d 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.
 2020-03-21 22:11:25 +00:00
Joseph Mingrone
586a7eaabb biology/diamond: Update to version 0.9.30 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.30
 2020-02-03 15:55:05 +00:00
Joseph Mingrone
8eb84e2015 biology/diamond: Update to v0.9.29 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.29
 2019-11-20 17:14:29 +00:00
Joseph Mingrone
47738adc67 biology/diamond: Update to version 0.9.28 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.28
 2019-11-07 14:12:07 +00:00
Joseph Mingrone
cf2251f192 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
 2019-11-03 01:34:11 +00:00
Joseph Mingrone
1aeb4149fc biology/diamond: Update to version 0.9.26 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.26
 2019-09-18 18:45:09 +00:00
Mathieu Arnold
a6c40a689b Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
Joseph Mingrone
4d67ec8def biology/diamond: Update to version 0.9.25 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.25
 2019-08-04 23:35:15 +00:00
Joseph Mingrone
3b7c3a4880 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
 2018-12-31 19:00:00 +00:00
Tobias C. Berner
707c6bf295 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
 2018-12-25 20:25:39 +00:00
Joseph Mingrone
c9ff93b67d 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
 2018-12-17 19:12:38 +00:00
Joseph Mingrone
3a8df683d4 biology/diamond: Update to version 0.9.22 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.22
 2018-05-14 17:17:11 +00:00
Joseph Mingrone
0ec83055e0 biology/diamond: Update to version 0.9.21 
Upstream changes: https://github.com/bbuchfink/diamond/releases
 2018-04-20 21:23:27 +00:00
Joseph Mingrone
763d42349c biology/diamond: Update to version 0.9.19 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.19
 2018-03-17 15:29:13 +00:00
Joseph Mingrone
94e4c0f0fb 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
 2018-03-15 02:28:09 +00:00
Joseph Mingrone
bcc328fe9b biology/diamond: Update to version 0.9.17 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.17
 2018-02-01 19:20:07 +00:00
Joseph Mingrone
390c5f7f64 biology/diamond: Update to version 0.9.14 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.14
 2017-12-13 16:31:53 +00:00
Joseph Mingrone
6ce3a81f62 biology/diamond: Update to version 0.9.13 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.13
 2017-11-17 20:11:05 +00:00
Joseph Mingrone
587f788379 biology/diamond: Update to version 0.9.12 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.12
 2017-11-08 16:06:50 +00:00
Joseph Mingrone
a29978a882 biology/diamond: Update to 0.9.11 
Upstream changes: https://github.com/bbuchfink/diamond/releases
 2017-11-03 03:45:01 +00:00
Joseph Mingrone
5308546037 biology/diamond: Update to version 0.9.10 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.10
 2017-08-15 20:45:08 +00:00
Joseph Mingrone
7b52e9ffb8 biology/diamond: Update to version 0.9.9 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.9
 2017-07-03 19:12:18 +00:00
Joseph Mingrone
c08b519ed5 biology/diamond: Update to version 0.9.8 2017-06-16 14:49:19 +00:00
Joseph Mingrone
9f1a4d5a79 biology/diamond: Update to version 0.9.4 
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.4
 2017-06-03 12:32:15 +00:00
Joseph Mingrone
d4837420de biology/diamond: Update to version 0.9.3 
Upstream changes: https://github.com/bbuchfink/diamond/releases

Approved by:	swills (mentor, implicit)
 2017-05-29 15:24:01 +00:00
Joseph Mingrone
addf5b1511 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)
 2017-05-23 11:03:08 +00:00
Joseph Mingrone
09e24ad52a 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)
 2017-04-21 14:46:07 +00:00
Joseph Mingrone
37aa0c5071 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)
 2017-04-02 10:55:31 +00:00
Gerald Pfeifer
04d6f52202 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
 2017-04-01 15:23:30 +00:00
Joseph Mingrone
160fb7edd1 biology/diamond: Update to version 0.8.36. 
Approved by:	swills (mentor, implicit)
 2017-02-12 14:04:57 +00:00
Joseph Mingrone
696ac89fbd biology/diamond: Update to version 0.8.35. 
Version 0.8.35 fixes a compiler error on i386.

Approved by:	swills (mentor, implicit)
 2017-02-05 22:23:32 +00:00
Joseph Mingrone
6999e8c7ba 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
 2017-01-23 13:19:17 +00:00
Joseph Mingrone
bdad5154e4 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
 2017-01-16 13:38:12 +00:00
Joseph Mingrone
ac30d1f025 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
 2017-01-12 23:23:19 +00:00
Joseph Mingrone
ff75dda797 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
 2016-12-30 16:27:25 +00:00