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3427 commits

Author SHA1 Message Date
Yuri Victorovich
56003e73b8 biology/figtree: Update 1.4.4 -> 1.4.4-14 2022-08-27 22:52:00 -07:00
Joseph Mingrone
5aec6e4a19
biology/paml: Update to 4.10.5 
https://github.com/abacus-gene/paml/releases/tag/v4.10.0
https://github.com/abacus-gene/paml/releases/tag/untagged-a5659203e8ec0ddb58b8
https://github.com/abacus-gene/paml/releases/tag/v4.10.5

Sponsored by:	The FreeBSD Foundation
 2022-08-26 01:22:46 -03:00
Yuri Victorovich
cd42c21b03 biology/kmcp: Update 0.8.3 -> 0.8.4 2022-08-18 11:56:49 -07:00
Yuri Victorovich
98217ec7b7 biology/kmcp: Update 0.8.2 -> 0.8.3 2022-08-15 10:30:24 -07:00
Yuri Victorovich
a47d034514 biology/kmcp: Broken on i386 and arm64 
Reported by:	fallout
 2022-08-14 23:09:12 -07:00
Matthias Andree
875d7c7d19 *: bump PORTREVISION of all devel/xxhash users... 
...except archivers/py-borgbackup, which requires a more complete fix.
 2022-08-13 20:51:14 +02:00
Dima Panov
4cf39decb3 */*: bump all consumers after recent boost upgrade 2022-08-12 17:46:53 +03:00
Dmitry Marakasov
b28e6ccdb9 biology/gatk: mark BROKEN 
FAILURE: Build failed with an exception.

* Where:
Build file '/wrkdirs/usr/ports/biology/gatk/work/gatk-4.2.6.1/build.gradle' line: 15

* What went wrong:
Plugin [id: 'de.undercouch.download', version: '4.1.2'] was not found in any of the following sources:

- Gradle Core Plugins (plugin is not in 'org.gradle' namespace)
- Plugin Repositories (could not resolve plugin artifact 'de.undercouch.download:de.undercouch.download.gradle.plugin:4.1.2')
  Searched in the following repositories:
    Gradle Central Plugin Repository

Reported by:	pkg-fallout
Approved by:	portmgr blanket
 2022-08-11 21:33:41 +03:00
Yuri Victorovich
d17e67375d biology/kmcp: New port: Accurate metagenomic profiling & fast large-scale genome searching 2022-08-07 13:30:47 -07:00
Yuri Victorovich
183ec5cd65 biology/ncbi-cxx-toolkit: Broken on armv6 
Reported by:	fallout
 2022-08-06 16:28:43 -07:00
Yuri Victorovich
425afd9918 biology/hyphy: Update 2.5.40 -> 2.5.41 
PR:		265677
Approved by:	jrm@ (maintainer)
 2022-08-06 15:23:11 -07:00
Yuri Victorovich
a93cd97f3c biology/py-ete3: Add tests 2022-08-06 15:23:11 -07:00
Yuri Victorovich
5d1325cd1b biology/ugene: Correct BROKEN message 
Approved by:	portmgr (blanket)
 2022-08-04 09:35:24 -07:00
Yuri Victorovich
36aeef9b99 biology/hyphy: Correct BROKEN message 2022-08-04 09:21:46 -07:00
Yuri Victorovich
efc6565174 biology/hhsuite: Fix build on some architectures 
... by removing -march=native.

Reported by:	fallout
 2022-08-04 09:21:45 -07:00
Yuri Victorovich
bd8b68e641 biology/hhsuite: Revert commit "Broken on systems where OpenMP isn't enabled" 
IT was added by mistake.
The failures on armv7 are due to -march=native.

This reverts commit 0f20e25bb0.

Reported by:	pkubaj@
 2022-08-04 09:21:45 -07:00
Yuri Victorovich
34c51b63d7 biology/ugene: Broken on systems where OpenMP isn't enabled 
Reported by:	fallout
Approved by:	portmgr (blanket)
 2022-08-04 00:41:24 -07:00
Yuri Victorovich
0f20e25bb0 biology/hhsuite: Broken on systems where OpenMP isn't enabled 
Reported by:	fallout
 2022-08-04 00:41:24 -07:00
Yuri Victorovich
6a6938ea10 biology/hyphy: Broken on systems where OpenMP isn't enabled 
Reported by:	fallout
Approved by:	portmgr (blanket)
 2022-08-04 00:41:22 -07:00
Dmitri Goutnik
4476f89764 all: Bump PORTREVISION after Go update 
Bump Go ports PORTREVISION after GO_DEFAULT and lang/go118 update.
 2022-08-03 16:35:13 -05:00
Yuri Victorovich
c7b296877c biology/viennarna: Update 2.5.0 -> 2.5.1 
Also add test target.
 2022-07-31 01:12:49 -07:00
Yuri Victorovich
5c534ae656 biology/abyss: Add test target 2022-07-30 00:34:34 -07:00
Po-Chuan Hsieh
8d5b2bc5bb
devel/grpc: Update to 1.48.0 
- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://github.com/grpc/grpc/releases
 2022-07-30 13:57:09 +08:00
Yuri Victorovich
0a752832a5 biology/abyss: Update 2.3.1 -> 2.3.5 2022-07-29 12:57:36 -07:00
Yuri Victorovich
62ffe981e3 biology/py-mrcfile: Update 1.4.0 -> 1.4.2 2022-07-29 01:46:46 -07:00
Yuri Victorovich
8fd55d46d9 biology/cufflinks: Unbreak 2022-07-27 20:43:06 -07:00
Yuri Victorovich
8832ed3498 biology/star: Broken on systems where OpenMP isn't enabled 
Reported by:	fallout
Approved by:	portmgr (blanket)
 2022-07-23 18:24:10 -07:00
Yuri Victorovich
8dc7394ac8 biology/molden: Update 6.7 -> 7.1 
PR:		265245
Approved by:	jmd@ (maintainer)
 2022-07-23 13:00:53 -07:00
Yuri Victorovich
280dd32be2 biology/mmseqs2: Not require OpenMP on systems where OpenMP isn't enabled 
Reported by:	fallout
Approved by:	portmgr (blanket)
 2022-07-23 09:40:43 -07:00
Yuri Victorovich
768fb66f82 biology/ngs-sdk: Broken on armv6, armv7 
Reported by:	fallout
 2022-07-22 15:34:07 -07:00
Tobias C. Berner
11049e36cb cleanup: remove '$MCom' tag 
gnome@ no longer uses Marcusom as their staging ground.

Approved by:		gnome (nc)
Differential Revision:	https://reviews.freebsd.org/D35866
 2022-07-20 21:44:12 +02:00
Tobias C. Berner
5564b3b420 science/hdf5: bump PORTREVISION of consumers 
The SO-version increased in the update to 1.12.2 in
a43418b815 .

Reported by:	VVD <vvd@unislabs.com>
 2022-07-20 16:35:24 +02:00
Tobias C. Berner
37526bbd4e biology: remove 'Created by' lines 
A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
  *  Johann Visagie <johann@egenetics.com>
  *  Johann Visagie <wjv@FreeBSD.org>
  *  Mauricio Herrera Cuadra <mauricio@arareko.net>
  *  Motomichi Matsuzaki <mzaki@biol.s.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@e-mail.ne.jp>
  *  Motomichi Matsuzaki <mzaki@m.u-tokyo.ac.jp>
  *  Motomichi Matsuzaki <mzaki@niid.go.jp>
  *  Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Razi Khaja <razi@genet.sickkids.on.ca>
  *  Reed A. Cartwright <cartwright@asu.edu>
  *  Ryo MIYAMOTO
  *  Ryo MIYAMOTO <rmiya@cc.hirosaki-u.ac.jp>
  *  Sangwoo Shim <sangwoos@gmail.com>
  *  Sunpoet Po-Chuan Hsieh <sunpoet@FreeBSD.org>
  *  Tassilo Philipp <tphilipp@potion-studios.com>
  *  Tony Maher
  *  Tony Maher <tonym@biolateral.com.au>
  *  Wen Heping <wen@FreeBSD.org>
  *  Wen Heping <wenheping@gmail.com>
  *  Yonatan <onatan@gmail.com>
  *  Yuri Victorovich <yuri@rawbw.com>
  *  ballen
  *  barnhart@genetics.wustl.edu
  *  camson@bilateral.com.au
  *  chuynh@biolateral.com.au
  *  dbader@eece.unm.edu
  *  frankch@waru.life.nthu.edu.tw
  *  h2
  *  lentferj
  *  maho@FreeBSD.org
  *  mzaki@biol.s.u-tokyo.ac.jp
  *  tonym
  *  wen@FreeBSD.org

With hat:	portmgr
 2022-07-20 16:20:57 +02:00
Yuri Victorovich
978fbbf602 biology/py-pysam: Remove BROKEN lines 2022-07-19 08:51:56 -07:00
Yuri Victorovich
8e9198d404 biology/py-pysam: Fix on aarch64, riscv6 by backporting of symbols failure fix 2022-07-19 08:51:55 -07:00
Yuri Victorovich
09d9d827a5 biology/py-pysam: Correct BROKEN line; Add comment 2022-07-18 19:09:00 -07:00
Joseph Mingrone
c886234c5a
biology/hyphy: Update to 2.5.40 
https://github.com/veg/hyphy/releases/tag/2.5.40
https://github.com/veg/hyphy/compare/2.5.39...2.5.40

Sponsored by:	The FreeBSD Foundation
 2022-07-18 12:40:25 -03:00
Po-Chuan Hsieh
ba66c05b01
biology/sra-tools: Fix build with HDF5 1.12.0+ 2022-07-18 20:50:17 +08:00
Po-Chuan Hsieh
7e7034a7fa
biology/ncbi-vdb: Fix build with HDF5 1.12.0+ 2022-07-18 20:50:17 +08:00
Yuri Victorovich
328d02d88e biology/molden: Unbreak build; Correct WWW 
For unbreak:
- pass FFLAGS to the build
- fix several errors in C
- remove the failing 'ex' command from makefile

Reported by:	fallout
Approved by:	portmgr (unbreak)
 2022-07-15 16:34:09 -07:00
Yuri Victorovich
2f374bcdfe biology/py-pysam: Broken on arm64 and riscv64 
Reported by:	fallout
 2022-07-14 19:45:53 -07:00
Dmitri Goutnik
153cb65ac8 all: Bump PORTREVISION after lang/go{117,118} update 2022-07-14 07:46:05 -05:00
Jason W. Bacon
bcc206f2be biology/pooler: Update to 1.85 
Change default annealing temperature from 37C to 45C

PR:             265163
Reported by:    silas-freebsd@flatline.org.uk
 2022-07-12 07:47:45 -05:00
Yuri Victorovich
d3e9586369 biology/ngs-sdk: Revert: Un-remove, ngs was moved into sra-tools 
This reverts commit 1cb8897f61.

sra-tools needs to be updated first.

Reported by:	Tomoaki AOKI <junchoon@dec.sakura.ne.jp>, perciva@
 2022-07-06 18:33:58 -07:00
Yuri Victorovich
5fa506511a biology/gcta: Use bundled version of eigen3 
... in preparation to upgrading math/eigen to 3.4.0.

This version of gcta (1.26.0) doesn't support eigen-3.4.0, and
it can't be upgraded because latest versions of gcta use
Intel's closed source MKL library.

PR:		265032
Suggested by:	tcberner@
Approved by:	portmgr (interoperability)
 2022-07-06 13:40:04 -07:00
Yuri Victorovich
1cb8897f61 biology/ngs-sdk: Remove, ngs was moved into sra-tools 2022-07-06 12:03:11 -07:00
Yuri Victorovich
2aa1d90e58 biology/py-mrcfile: Update 1.3.0 -> 1.4.0 
Reported by:	portscout
 2022-07-03 15:01:23 -07:00
Po-Chuan Hsieh
b1a61c790e
devel/grpc: Update to 1.47.0 
- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://github.com/grpc/grpc/releases
 2022-06-30 00:32:34 +08:00
Stefan Eßer
b52114270f Fix CONFLICTS_INSTALL in benchmarks and biology 
Approved by:	portmgr (implicit)
 2022-06-29 16:53:54 +02:00
Yuri Victorovich
5d253e6fc1 biology/seqan3: Update 3.1.0 -> 3.2.0 
Reported by:	portscout
 2022-06-24 00:20:46 -07:00