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3464 commits

Author SHA1 Message Date
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
Yuri Victorovich
2920285450 biology/biosig: Update 2.4.1 -> 2.4.2 
Reported by:	portscout
 2022-06-19 09:53:42 -07:00
Yuri Victorovich
db283c3063 biology/mopac: Move to science/mopac; Add TIMESTAMP to distinfo; Take maintainership 2022-06-19 00:52:28 -07:00
Po-Chuan Hsieh
328ae40742
*/*: Replace science/szip with science/libaec 
- Bump PORTREVISION of dependent ports for dependency change

szip does not allow redistribution in binary form without proper commercial
license. Its LICENSE_PERMS should be set to no-auto-accept which blocks building
this port, therefore building dependent ports are also blocked. Switch all
dependent ports to science/libaec to avoid conflicts and license issue.

PR:		228743, 246097, 250165
 2022-06-16 23:13:01 +08:00
Jason W. Bacon
a32ba8bb15 biology/vcf2hap: Update to 0.1.6 
Update for bl_vcf_t API streamlining

Changes:        https://github.com/auerlab/vcf2hap/tags
 2022-06-11 09:26:57 -05:00
Jason W. Bacon
620c716685 biology/peak-classifier: Update to 0.1.4 
Update for bl_gff_t API streamlining

Changes:        https://github.com/auerlab/peak-classifier/tags
 2022-06-11 09:26:57 -05:00
Jason W. Bacon
5e31c875e1 biology/ad2vcf: Update to 0.1.6 
Updates for bl_sam_t and bl_vcf_t API streamlining

Changes:        https://github.com/auerlab/ad2vcf/tags
 2022-06-11 09:26:57 -05:00
Jason W. Bacon
ef8583e1d5 biology/vcf-split: Update to 0.1.5 
Use stremalined biolibc API
Minor build system improvements

Changes:        https://github.com/auerlab/vcf-split/tags
 2022-06-11 09:26:56 -05:00
Jason W. Bacon
f869d6b412 biology/biolibc-tools: Update to 0.1.3 
Add vcf-downsample subcommand
Improvements to build system
extract-seq: Recurse to output subfeatures
Numerous other minor enhancements and fixes

Changes:        https://github.com/auerlab/biolibc-tools/tags
 2022-06-11 09:26:56 -05:00
Jason W. Bacon
603571cd32 biology/biolibc: Update to 0.2.3 
Expand use of tsv_read_field_malloc() to improve memory efficiency
Add SAM bit flag constants
Import SAM-GFF compare functions from diffanal
Updates for libxtend DSV API changes
Numerous minor bug fixes and enhancements

Changes:        https://github.com/auerlab/biolibc/tags
 2022-06-11 09:26:56 -05:00
Yuri Victorovich
2ddde7b75a biology/taxonkit: Update 0.11.1 -> 0.12.0 
Reported by:	portscout
 2022-06-08 23:08:00 -07:00
Yuri Victorovich
5432af7303 biology/{,py-}libsedml: Update 2.0.31 -> 2.0.32 
Reported by:	portscout
 2022-06-08 22:53:28 -07:00
Dmitri Goutnik
309cdeccd8 */*: Bump port revisons after lang/go{117,118} update 2022-06-07 16:56:10 -05:00
Yuri Victorovich
97850626d5 biology/py-resdk: Update 14.1.0 -> 15.0.0 
Reported by:	portscout
 2022-06-06 17:38:49 -07:00
Yuri Victorovich
e93a47c484 biology/py-gffutils: Update 0.10.1 -> 0.11.0 
Reported by:	portscout
 2022-06-06 17:38:48 -07:00
Dmitri Goutnik
b16eb860cc */*: Repair after switching to versioned Go ports 
- Add 1.17 to USES=go for ports that still need go117, remove GO_PORT;
- Add missing ${SETENV} ${MAKE_ENV} to repair BINARY_ALIAS;
- Remove explicit dependencies on lang/go.

PR:		264336
Reviewed by:	ygy jwb yuri mikael drtr0jan@yandex.ru decke mat
Differential Revision:	https://reviews.freebsd.org/D35346
 2022-06-06 13:19:10 -05:00
Yuri Victorovich
45c4e1c9f3 biology/py-scikit-bio: Broken on aarch64 
Reported by:	fallout
 2022-06-03 15:56:03 -07:00
Yuri Victorovich
e8c0b45474 biology/py-pysam: Update 0.19.0 -> 0.19.1 
Reported by:	portscout
 2022-05-30 17:23:32 -07:00
Joseph Mingrone
f519fe65ca
biology/hyphy: Update to 2.5.39 
https://github.com/veg/hyphy/releases/tag/2.5.39hf1

Sponsored by:	The FreeBSD Foundation
 2022-05-26 23:38:12 -03:00
Yuri Victorovich
2c5f8b153e biology/gatk: Use Java 17 instead of EOLed Java 12 2022-05-24 15:39:38 -07:00
Rene Ladan
c7d1c247d8 cleanup: remove expired versions of OpenJDK (12 through 16) 
Adjust ports depending on expired versions of OpenJDK:
- biology/snpeff: 12+ -> 17+
- devel/RStudio: 12 -> 11
- www/closure-compiler: 13 -> 11+

Allow java/openjdk17 to use java/openjdk17-bootstrap on i386
too, this builds just fine on 13.1-i386

Remove jdk12-doc as it is no longer relevant.

Clean up Java version calculations in bsd.java.mk

Reviewed by: jwb, java (glewis)

Differential Revision: https://reviews.freebsd.org/D35280
 2022-05-24 22:09:35 +02:00
Yuri Victorovich
64c437262d biology/gatk: Update 4.2.6.0 -> 4.2.6.1 2022-05-22 19:05:40 -07:00
Dima Panov
b082b3d13e devel/boost-all: bump all library consumers after boost upgrade 
PR:	246106
 2022-05-22 23:17:16 +03:00
Dima Panov
1054b6f30e biology/cufflinks: mark as BROKEN after recent boost upgrade 
PR:	246106
 2022-05-22 23:17:09 +03:00
Yuri Victorovich
8b4b845a51 biology/py-PySCeS: Update 1.0.1 -> 1.0.2 
Reported by:	portscout
 2022-05-20 15:02:59 -07:00
Yuri Victorovich
5ba960dcdd biology/taxonkit: Update 0.11.0 -> 0.11.1 
Reported by:	portscout
 2022-05-20 15:02:59 -07:00
Yuri Victorovich
a19ac12c2c biology/mothur: Update 1.47.0 -> 1.48.0 
Reported by:	portscout
 2022-05-19 19:10:18 -07:00
Yuri Victorovich
d776c97dcf biology/biosig: Update 2.4.0 -> 2.4.1 2022-05-16 15:09:25 -07:00
Yuri Victorovich
8732b987ed biology/taxonkit: Update 0.10.1 -> 0.11.0 
Reported by:	portscout
 2022-05-16 11:45:25 -07:00
Loïc Bartoletti
2d34c2bfea devel/cmake: Update to 3.23.0 
Update to 3.23.0.
Fix pkg-plist: using the default share/man location

Release Notes:
  https://cmake.org/cmake/help/v3.23/release/3.23.html

PR:		262886
Exp-run by:	antoine
 2022-05-16 08:49:43 +02:00
Po-Chuan Hsieh
bf3c49f70a
devel/grpc: Update to 1.46.0 
- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://github.com/grpc/grpc/releases
 2022-05-13 19:39:14 +08:00
Kevin Bowling
db78da8f8b devel/libffi: Bump deps PORTREVISION for shlib change 
PR:		263764
Reported by:	VVD <vvd@unislabs.com>
 2022-05-09 12:23:51 -07:00
Jason W. Bacon
dda5e52508 biology/py-dna-features-viewer: Update to 3.1.1 
python 3.9 compatibility

Changes: https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/tags

Reported by:    portscout
 2022-05-08 07:48:38 -05:00
Yuri Victorovich
dda16bd485 biology/checkm: Update 1.1.11 -> 1.2.0 
Reported by:	portscout
 2022-05-01 11:14:09 -07:00
Yuri Victorovich
8db0b60850 biology/py-mrcfile: New port: MRC file I/O library which is used in structural biology 2022-05-01 10:37:04 -07:00
Yuri Victorovich
84de6204b9 biology/py-pysam: Update 0.18.0 -> 0.19.0 
Reported by:	portscout
 2022-04-27 10:38:26 -07:00
Yuri Victorovich
fedffc237c biology/py-resdk: Update 14.0.0 -> 14.1.0 
Reported by:	portscout
 2022-04-27 10:38:25 -07:00
Piotr Kubaj
eaf43a218b biology/pooler: use openmp only when omp.h is present 2022-04-27 13:22:12 +00:00
Piotr Kubaj
1115257612 biology/ncbi-blast+: check for omp.h on all architectures 2022-04-27 13:22:09 +00:00
Piotr Kubaj
74016ad026 biology/cd-hit: check for omp.h on all architectures 2022-04-27 13:22:07 +00:00
Piotr Kubaj
e7af5e32b4 biology/hhsuite: check for omp.h on all architectures 2022-04-27 13:22:04 +00:00
Piotr Kubaj
cf150ef9e2 biology/fasttree: check for omp.h on all architectures 2022-04-27 13:22:02 +00:00
Yuri Victorovich
a47cbfbf39 biology/unikmer: Update 0.18.8 -> 0.19.0 
Reported by:	portscout
 2022-04-26 11:51:57 -07:00
Yuri Victorovich
088dbf75b8 biology/checkm: Update 1.1.10 -> 1.1.11 
Reported by:	portscout
 2022-04-25 13:50:10 -07:00
Piotr Kubaj
b3b6b26431 biology/seqan-apps: remove obsolete USE_GCC 
Instead use USES=compiler.
 2022-04-25 14:12:52 +00:00
Joseph Mingrone
e2c4d38d48
biology/hyphy: Update to 2.5.38 
Upstream changes: https://github.com/veg/hyphy/compare/2.5.36...2.5.38

Sponsored by:	The FreeBSD Foundation
 2022-04-24 15:24:30 -03:00
Joseph Mingrone
d9f5d5d949
biology/diamond: Update to 2.0.15 
https://github.com/bbuchfink/diamond/releases/tag/v2.0.15

Sponsored by:	The FreeBSD Foundation
 2022-04-24 14:50:21 -03:00
Yuri Victorovich
2d70d2a28e biology/{,py-}libnuml: Update 1.1.5 -> 1.1.6 
Reported by:	portscout
 2022-04-23 18:36:56 -07:00
Yuri Victorovich
1c92a5a1da biology/{,py-}libsedml: Update 2.0.30 -> 2.0.31 
Reported by:	portscout
 2022-04-22 11:04:38 -07:00
Yuri Victorovich
d0a1dad5c4 biology/checkm: Update 1.1.9 -> 1.1.10 
Reported by:	portscout
 2022-04-22 11:04:37 -07:00
Piotr Kubaj
8a75ffbc9f biology/hhsuite: drop HAVE_POWER8 on powerpc64 
powerpc64 uses PPC970 as a baseline.
 2022-04-21 17:11:16 +00:00
Piotr Kubaj
52e46764cf biology/py-scikit-bio: drop unnecessary USE_GCC on powerpc64 2022-04-21 17:11:15 +00:00
Piotr Kubaj
6812895caa biology/bolt-lmm: remove unnecessary CFLAGS_powerpc64 2022-04-21 17:11:13 +00:00
Yuri Victorovich
44210d2f50 biology/seqkit: Update 2.1.0 -> 2.2.0 
Reported by:	portscout
 2022-04-19 20:44:55 -07:00
Piotr Kubaj
a3f5e20929 biology/py-scikit-bio: build with clang on powerpc64le 2022-04-19 14:09:20 +02:00
Piotr Kubaj
b48c8810a8 biology/bolt-lmm: remove unnecessary flags for powerpc64le 2022-04-17 13:05:53 +02:00
Yuri Victorovich
f7875ce1de biology/checkm: Update 1.1.8 -> 1.1.9 
Reported by:	portscout
 2022-04-15 12:09:58 -07:00
Yuri Victorovich
1aa4b19950 biology/py-scikit-bio: Update 0.5.6 -> 0.5.7 
Reported by:	portscout
 2022-04-15 12:09:57 -07:00
Yuri Victorovich
350d96226d biology/checkm: Update 1.0.18 -> 1.1.8 
Reported by:	portscout
 2022-04-11 20:22:30 -07:00
Yuri Victorovich
0fe062bee9 biology/gatk: Update 4.2.0.0 -> 4.2.6.0 2022-04-10 16:21:50 -07:00
Charlie Li
d63665f7cd
textproc/libxml2: bump all LIB_DEPENDS consumers 
This is a separate commit to facilitate easier cherry-picking for
quarterly.

PR: 262853, 262940, 262877, 263126
Approved by: fluffy (mentor)
 2022-04-10 15:11:41 -04:00
Yuri Victorovich
53aca1ad84 biology/{,py-}libsedml: Update 2.0.28 -> 2.0.30 
Reported by:	portscout
 2022-04-07 13:19:03 -07:00
Yuri Victorovich
0ba58a1a6f biology/{,py-}libnuml: Update 1.1.4 -> 1.1.5 
Reported by:	portscout
 2022-04-07 13:19:03 -07:00
Dmitry Marakasov
ff5a2c36cc biology/py-cutadapt: fix tests by adding missing test depend 
Approved by:	portmgr blanket
 2022-04-07 21:59:32 +03:00