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Port details
diamond BLAST-compatible local sequence aligner
0.9.8 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 06 May 2016 08:45:09
License: AGPLv3
DIAMOND is a BLAST-compatible local aligner for mapping protein and translated
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/
SVNWeb : Homepage : PortsMon

To install the port: cd /usr/ports/biology/diamond/ && make install clean
To add the package: pkg install diamond

PKGNAME: diamond

ONLY_FOR_ARCHS: amd64 i386

distinfo:

TIMESTAMP = 1497624129
SHA256 (bbuchfink-diamond-v0.9.8_GH0.tar.gz) = 435a56a9d4c383bf560a640c9c5da44a5200661808184b968825c5217700c511
SIZE (bbuchfink-diamond-v0.9.8_GH0.tar.gz) = 385760


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. cmake : devel/cmake
There are no ports dependent upon this port

Configuration Options
     No options to configure

USES:
cmake:outsource

Master Sites:
  1. https://codeload.github.com/bbuchfink/diamond/tar.gz/v0.9.8?dummy=/

Number of commits found: 33

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
16 Jun 2017 14:49:19
Original commit files touched by this commit  0.9.8
Revision:443706
jrm search for other commits by this committer
biology/diamond: Update to version 0.9.8
03 Jun 2017 12:32:16
Original commit files touched by this commit  0.9.4
Revision:442478
jrm search for other commits by this committer
biology/diamond: Update to version 0.9.4

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.4
29 May 2017 15:24:01
Original commit files touched by this commit  0.9.3
Revision:441991
jrm search for other commits by this committer
biology/diamond: Update to version 0.9.3

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

Approved by:	swills (mentor, implicit)
23 May 2017 11:03:09
Original commit files touched by this commit  0.9.1
Revision:441513
jrm search for other commits by this committer
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)
21 Apr 2017 14:46:07
Original commit files touched by this commit  0.8.38
Revision:439081
jrm search for other commits by this committer
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)
02 Apr 2017 10:55:31
Original commit files touched by this commit  0.8.37
Revision:437552
jrm search for other commits by this committer
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)
01 Apr 2017 15:23:32
Original commit files touched by this commit  0.8.36_1
Revision:437439
gerald search for other commits by this committer
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
12 Feb 2017 14:04:57
Original commit files touched by this commit  0.8.36
Revision:433945
jrm search for other commits by this committer
biology/diamond: Update to version 0.8.36.

Approved by:	swills (mentor, implicit)
05 Feb 2017 22:23:32
Original commit files touched by this commit  0.8.35
Revision:433463
jrm search for other commits by this committer
biology/diamond: Update to version 0.8.35.

Version 0.8.35 fixes a compiler error on i386.

Approved by:	swills (mentor, implicit)
23 Jan 2017 13:19:18
Original commit files touched by this commit  0.8.34
Revision:432214
jrm search for other commits by this committer
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
16 Jan 2017 13:38:12
Original commit files touched by this commit  0.8.32
Revision:431644
jrm search for other commits by this committer
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
12 Jan 2017 23:23:19
Original commit files touched by this commit  0.8.31
Revision:431331
jrm search for other commits by this committer
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
30 Dec 2016 16:27:25
Original commit files touched by this commit  0.8.30
Revision:429998
jrm search for other commits by this committer
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
18 Dec 2016 13:52:32
Original commit files touched by this commit  0.8.29
Revision:428850
jrm search for other commits by this committer
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
28 Nov 2016 15:18:15
Original commit files touched by this commit  0.8.28
Revision:427328
jrm search for other commits by this committer
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
06 Nov 2016 05:42:32
Original commit files touched by this commit  0.8.26
Revision:425464
jrm search for other commits by this committer
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
17 Oct 2016 14:17:19
Original commit files touched by this commit  0.8.24
Revision:424118
jrm search for other commits by this committer
biology/diamond: update to version 0.8.24

Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D8268
10 Oct 2016 04:33:16
Original commit files touched by this commit  0.8.23
Revision:423635
jrm search for other commits by this committer
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
23 Sep 2016 21:42:02
Original commit files touched by this commit  0.8.22
Revision:422697
jrm search for other commits by this committer
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
13 Sep 2016 17:50:31
Original commit files touched by this commit  0.8.22
Revision:422046
amdmi3 search for other commits by this committer
- Update to 0.8.22

PR:		212603
Submitted by:	jrm@ftfl.ca (maintainer)
06 Sep 2016 06:34:59
Original commit files touched by this commit  0.8.20
Revision:421406
wen search for other commits by this committer
- Update to 0.8.20

PR:		212399
Submitted by:	jrm@ftfl.ca(maintainer)
25 Aug 2016 18:49:12
Original commit files touched by this commit  0.8.19
Revision:420873
pawel search for other commits by this committer
Update to version 0.8.19

PR:		212145
Submitted by:	Joseph Mingrone (maintainer)
14 Aug 2016 21:47:57
Original commit files touched by this commit  0.8.18
Revision:420200
brd search for other commits by this committer
Update biology/diamond to 0.8.18.

PR:		211845
Submitted by:	Joseph Mingrone <jrm@ftfl.ca> (maintainer)
Approved by:	bdrewery (implicit)
05 Aug 2016 21:24:06
Original commit files touched by this commit  0.8.17
Revision:419710
pawel search for other commits by this committer
Update to version 0.8.17

PR:		211582
Submitted by:	Joseph Mingrone (maintainer)
24 Jul 2016 18:06:21
Original commit files touched by this commit  0.8.16
Revision:419014
riggs search for other commits by this committer
Update to upstream release 0.8.16

PR:		211335
Submitted by:	jrm@ftfl.ca (maintainer)
14 Jul 2016 16:53:06
Original commit files touched by this commit  0.8.14
Revision:418546
pawel search for other commits by this committer
Trim excess tabs, no-op change
14 Jul 2016 16:49:41
Original commit files touched by this commit  0.8.14
Revision:418544
pawel search for other commits by this committer
Update to version 0.8.14

PR:		211078
Submitted by:	Joseph Mingrone (maintainer)
07 Jul 2016 15:46:12
Original commit files touched by this commit  0.8.11
Revision:418187
amdmi3 search for other commits by this committer
- Update to 0.8.11

PR:		210877
Submitted by:	jrm@ftfl.ca (maintainer)
30 Jun 2016 01:37:22
Original commit files touched by this commit  0.8.9
Revision:417803
junovitch search for other commits by this committer
biology/diamond: update 0.8.6 -> 0.8.9

PR:		210710
Submitted by:	Joseph Mingrone <jrm@ftfl.ca> (maintainer)
17 Jun 2016 19:53:46
Original commit files touched by this commit  0.8.6
Revision:417033
rm search for other commits by this committer
biology/diamond: update to 0.8.6

PR:		210345
Submitted by:	Joseph Mingrone <jrm@ftfl.ca> (maintainer)
09 Jun 2016 01:39:58
Original commit files touched by this commit  0.8.5
Revision:416575
matthew search for other commits by this committer
Update to 0.8.5

PR:		209611
Submitted by:	jrm@ftfl.ca (maintainer)
18 May 2016 16:22:07
Original commit files touched by this commit  0.7.12_1
Revision:415454
antoine search for other commits by this committer
Fix DEPENDS
06 May 2016 08:45:02
Original commit files touched by this commit  0.7.12
Revision:414686
wen search for other commits by this committer
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: 33

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