non port: biology/diamond/Makefile |
Number of commits found: 87 |
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 |
Friday, 29 Dec 2023
|
18:57 Joseph Mingrone (jrm) Author: Dimitry Andric
biology/diamond: Fix build on main after import of clang 17
96286fc |
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
|
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
|
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 |
Wednesday, 7 Sep 2022
|
21:10 Stefan Eßer (se)
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.
This commit implements such a proposal and moves one of the WWW: entries
of each pkg-descr file into the respective port's Makefile. A heuristic
attempts to identify the most relevant URL in case there is more than
one WWW: entry in some pkg-descr file. URLs that are not moved into the
Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr
files in order to preserve them.
There are 1256 ports that had no WWW: entries in pkg-descr files. These
ports will not be touched in this commit.
The portlint port has been adjusted to expect a WWW entry in each port
Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as
deprecated.
Approved by: portmgr (tcberner)
b7f0544 |
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
|
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
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15:40 Joseph Mingrone (jrm)
biology/diamond: Update to 2.0.12
https://github.com/bbuchfink/diamond/releases/tag/v2.0.12
523d253 |
Saturday, 9 Oct 2021
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13:49 Piotr Kubaj (pkubaj)
biology/diamond: enable on powerpc64le
b6994df |
Friday, 8 Oct 2021
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18:19 Piotr Kubaj (pkubaj)
biology/diamond: enable on powerpc64
096fef4 |
16:25 Mikael Urankar (mikael)
biology/diamond: Enable on aarch64.
63de6c3 |
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
|
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
|
00:55 Joseph Mingrone (jrm)
biology/diamond: Update to 2.0.9
https://github.com/bbuchfink/diamond/releases/tag/v2.0.9
46fc7df |
Wednesday, 7 Apr 2021
|
08:09 Mathieu Arnold (mat)
One more small cleanup, forgotten yesterday.
Reported by: lwhsu
cf118cc |
Tuesday, 6 Apr 2021
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14:31 Mathieu Arnold (mat)
Remove # $FreeBSD$ from Makefiles.
305f148 |
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
|
Sunday, 30 Aug 2020
|
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
|
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
|
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.
|
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
|
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
|
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
|
Wednesday, 18 Sep 2019
|
18:45 jrm
biology/diamond: Update to version 0.9.26
Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.26
|
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
|
Monday, 31 Dec 2018
|
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
|
Tuesday, 25 Dec 2018
|
20:25 tcberner
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
|
Monday, 17 Dec 2018
|
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
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Thursday, 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
|
Thursday, 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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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
|
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
|
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
|
14:49 jrm
biology/diamond: Update to version 0.9.8
|
Saturday, 3 Jun 2017
|
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
|
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)
|
Saturday, 1 Apr 2017
|
15:23 gerald
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
|
Sunday, 12 Feb 2017
|
14:04 jrm
biology/diamond: Update to version 0.8.36.
Approved by: swills (mentor, implicit)
|
Sunday, 5 Feb 2017
|
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
|
Friday, 23 Sep 2016
|
21:42 jrm
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
|
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)
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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
|
16:53 pawel
Trim excess tabs, no-op change
|
16:49 pawel
Update to version 0.8.14
PR: 211078
Submitted by: Joseph Mingrone (maintainer)
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Thursday, 7 Jul 2016
|
15:46 amdmi3
- Update to 0.8.11
PR: 210877
Submitted by: jrm@ftfl.ca (maintainer)
|
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)
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Wednesday, 18 May 2016
|
16:22 antoine
Fix DEPENDS
|
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: 87 |