biology/diamond: Update to 2.1.11

Release notes:	https://github.com/bbuchfink/diamond/releases/tag/v2.1.11
Sponsored by:	The FreeBSD Foundation

biology/diamond: Update to v2.1.10

Release notes:	https://github.com/bbuchfink/diamond/releases/tag/v2.1.10
Sponsored by:	The FreeBSD Foundation

biology/diamond: Update to 2.1.9

Changelog:	https://github.com/bbuchfink/diamond/releases/tag/v2.1.9
Sponsored by:	The FreeBSD Foundation

biology/diamond: Fix build on main after import of clang 17

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

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

biology/diamond: Update to 2.1.4

Changes:	https://github.com/bbuchfink/diamond/releases/tag/v2.1.4
Sponsored by:	The FreeBSD Foundation

biology/diamond: Update to 2.1.3

Changes:	https://github.com/bbuchfink/diamond/releases/tag/v2.1.3
Sponsored by:	The FreeBSD Foundation

biology/diamond: Update to 2.1.2

Changes:	https://github.com/bbuchfink/diamond/releases/tag/v2.1.2
Sponsored by:	The FreeBSD Foundation

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

Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)

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.

biology/diamond: Update to 2.0.15

https://github.com/bbuchfink/diamond/releases/tag/v2.0.15

Sponsored by:	The FreeBSD Foundation

biology/diamond: Update to 2.0.14

https://github.com/bbuchfink/diamond/releases/tag/v2.0.14

Sponsored by:	The FreeBSD Foundation

biology/diamond: Update to 2.0.13

This update fixes a bug that caused invalid bit scores in frameshift
alignment mode.

biology/diamond: Update to 2.0.12

https://github.com/bbuchfink/diamond/releases/tag/v2.0.12

biology/diamond: enable on powerpc64le

biology/diamond: enable on powerpc64

biology/diamond: Enable on aarch64.

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

biology/diamond: Update to 2.0.10

https://github.com/bbuchfink/diamond/releases/tag/v2.0.10

biology/diamond: Update to 2.0.9

https://github.com/bbuchfink/diamond/releases/tag/v2.0.9

One more small cleanup, forgotten yesterday.
Reported by:	lwhsu

Remove # $FreeBSD$ from Makefiles.

biology/diamond: Update to 2.0.8

https://github.com/bbuchfink/diamond/releases/tag/v2.0.8

biology/diamond: Update to 2.0.7

https://github.com/bbuchfink/diamond/releases/tag/v2.0.7

biology/diamond: Update to version 2.0.6

https://github.com/bbuchfink/diamond/releases/tag/v2.0.6

biology/diamond: Update to version 2.0.5

https://github.com/bbuchfink/diamond/releases/tag/v2.0.5

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

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

biology/diamond: Update to version 2.0.0

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v2.0.0

biology/diamond: Update to version 0.9.36

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.36

biology/diamond: Update to version 0.9.35

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.35

biology/diamond: Update to version 0.9.34

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.34

biology/diamond: Update to version 0.9.33

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.33

biology/diamond: Update to version 0.9.32

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.32

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.

biology/diamond: Update to version 0.9.30

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.30

biology/diamond: Update to v0.9.29

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.29

biology/diamond: Update to version 0.9.28

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.28

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

biology/diamond: Update to version 0.9.26

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.26

Convert to UCL & cleanup pkg-message (categories a-c)

biology/diamond: Update to version 0.9.25

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.25

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

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

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

biology/diamond: Update to version 0.9.22

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.22

biology/diamond: Update to version 0.9.21

Upstream changes: https://github.com/bbuchfink/diamond/releases

biology/diamond: Update to version 0.9.19

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.19

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

biology/diamond: Update to version 0.9.17

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.17

biology/diamond: Update to version 0.9.14

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.14

biology/diamond: Update to version 0.9.13

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.13

biology/diamond: Update to version 0.9.12

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.12

biology/diamond: Update to 0.9.11

Upstream changes: https://github.com/bbuchfink/diamond/releases

biology/diamond: Update to version 0.9.10

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.10

biology/diamond: Update to version 0.9.9

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.9

biology/diamond: Update to version 0.9.8

biology/diamond: Update to version 0.9.4

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.4

biology/diamond: Update to version 0.9.3

Upstream changes: https://github.com/bbuchfink/diamond/releases

Approved by:	swills (mentor, implicit)

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)

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)

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)

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

biology/diamond: Update to version 0.8.36.

Approved by:	swills (mentor, implicit)

biology/diamond: Update to version 0.8.35.

Version 0.8.35 fixes a compiler error on i386.

Approved by:	swills (mentor, implicit)

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

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

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

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

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

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

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

biology/diamond: update to version 0.8.24

Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8268

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

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

- Update to 0.8.22

PR:		212603
Submitted by:	jrm@ftfl.ca (maintainer)

- Update to 0.8.20

PR:		212399
Submitted by:	jrm@ftfl.ca(maintainer)

Update to version 0.8.19

PR:		212145
Submitted by:	Joseph Mingrone (maintainer)

Update biology/diamond to 0.8.18.

PR:		211845
Submitted by:	Joseph Mingrone <jrm@ftfl.ca> (maintainer)
Approved by:	bdrewery (implicit)

Update to version 0.8.17

PR:		211582
Submitted by:	Joseph Mingrone (maintainer)

Update to upstream release 0.8.16

PR:		211335
Submitted by:	jrm@ftfl.ca (maintainer)

Trim excess tabs, no-op change

Update to version 0.8.14

PR:		211078
Submitted by:	Joseph Mingrone (maintainer)

- Update to 0.8.11

PR:		210877
Submitted by:	jrm@ftfl.ca (maintainer)

biology/diamond: update 0.8.6 -> 0.8.9

PR:		210710
Submitted by:	Joseph Mingrone <jrm@ftfl.ca> (maintainer)

biology/diamond: update to 0.8.6

PR:		210345
Submitted by:	Joseph Mingrone <jrm@ftfl.ca> (maintainer)

Update to 0.8.5

PR:		209611
Submitted by:	jrm@ftfl.ca (maintainer)

Fix DEPENDS

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