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3322 commits

Author SHA1 Message Date
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
Dmitry Marakasov
7b4d1f0b36 */*: fix trailing whitespace in pkg-descr's 
Approved by:	portmgr blanket
 2022-04-01 18:09:49 +03:00
Po-Chuan Hsieh
a478c75844
devel/grpc: Update to 1.45.0 
- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://github.com/grpc/grpc/releases
 2022-03-31 06:02:45 +08:00
Guangyuan Yang
d690b5102f */*: Bump PORTREVISION after lang/go 1.18 update 2022-03-30 03:01:44 -04:00
Matthias Fechner
247c7db751 textproc/libxml2: bump all dependencies 
This should make sure that all dependent ports will pick
up the new version commited with a13ec21cd7
 2022-03-26 09:27:27 +01:00
Jason W. Bacon
fad5d1754c biology/py-ont-fast5-api: Update to 4.0.2 
Minor bug fix release

Also disabled install of test directory, which was not properly
installed under the package subdir and caused a conflict as a result

PR:             262759
 2022-03-25 11:37:29 -05:00
Po-Chuan Hsieh
d1c57dce04
biology/python-nexus: Fix build with setuptools 58.0.0+ 
With hat:	python
 2022-03-25 21:38:05 +08:00
Po-Chuan Hsieh
0ffe3e7936
biology/py-crossmap: Fix build with setuptools 58.0.0+ 
With hat:	python
 2022-03-25 21:38:04 +08:00
Po-Chuan Hsieh
dab6c99caa
biology/groopm: Fix build with setuptools 58.0.0+ 
With hat:	python
 2022-03-25 21:38:04 +08:00
Po-Chuan Hsieh
c750cbac58
biology/checkm: Fix build with setuptools 58.0.0+ 
With hat:	python
 2022-03-25 21:38:04 +08:00
Yuri Victorovich
929ed69936 biology/dsr-pdb: Remove -pg (mcount instrumentation) flag 
This causes failure on aarch64: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=262709
 2022-03-21 17:07:11 -07:00
Jason W. Bacon
19264c9fb1 biology/fastq-trim: Update to 0.1.1.4 
Forgot to update fastq-vis -> fastq-scum in docs in previous update
 2022-03-21 16:19:36 -05:00
Jason W. Bacon
950fb7be37 biology/fastq-trim: Update to 0.1.1.2 
Replace crash with run with no arguments with help msg
fastq-vis -> fastq-scum (better name for contamination viewer)
 2022-03-21 15:37:43 -05:00
Yuri Victorovich
ed0ea3f134 biology/dsr-pdb: Broken on aarch64 
Reported by:	fallout
 2022-03-21 12:25:25 -07:00
Yuri Victorovich
b4062ba359 biology/biosig: Update 2.3.3 -> 2.4.0 
Reported by:	portscout
 2022-03-20 12:43:56 -07:00
Jason W. Bacon
0297052e22 biology/bolt-lmm: Update to 2.3.6 
Changes: https://alkesgroup.broadinstitute.org/BOLT-LMM/\
	 BOLT-LMM_manual.html#x1-60002.1

Also fixed build on aarch64: Replaced non-portable _mm_malloc() with
aligned_alloc()

Reported by:    pkg-fallout
 2022-03-20 10:29:01 -05:00
Jason W. Bacon
a47115b9ca biology/fastq-trim: Lightening fast sequence read trimmer 
Fastq-trim is a lightening fast read trimming tool for QA of
DNA and RNA reads prior to analyses such as RNA-Seq.
 2022-03-19 07:25:58 -05:00
Jason W. Bacon
52adc1acee biology/vcf2hap: Update to 0.1.5 
Minor update for biolibc 0.2.2 API changes
 2022-03-15 16:45:04 -05:00
Jason W. Bacon
58a9101d2b biology/vcf-split: Update to 0.1.4 
Minor update for biolibc 0.2.2 API changes
 2022-03-15 16:43:40 -05:00
Jason W. Bacon
aa7ea85d2b biology/peak-classifier: Update to 0.1.3 
Minor update for biolibc 0.2.2 API changes
 2022-03-15 16:41:51 -05:00
Jason W. Bacon
eab790a0c7 biology/ad2vcf: Update to 0.1.5 
Minor update for bioloibc 0.2.2 API changes
 2022-03-15 16:39:32 -05:00
Jason W. Bacon
b8604e856a biology/biolibc-tools: Update to 0.1.2 
New fastx-stats and ensembl2gene subcommands
Minor updates for biolibc 0.2.2 API changes
Minor bug fixes and ennancements
 2022-03-15 16:36:49 -05:00
Jason W. Bacon
258dc9d15d biology/biolibc: Update to 0.2.2 
Numerous bug fixes and enhancements
Serveral new functions
3 new classes
Cleaned up some API slop
Changes: https://github.com/auerlab/biolibc/tags
 2022-03-15 16:35:22 -05:00
Jason W. Bacon
3b861fa65f biology/pooler: Update to 1.84 
Bug fix for high core-count machines

PR:             232454
Reported by:    silas-freebsd@flatline.org.uk
 2022-03-14 09:41:38 -05:00
Rene Ladan
4e051b961c biology/gffread: remove local poudriere files 2022-03-07 23:44:38 +01:00
Po-Chuan Hsieh
58923d9729
devel/grpc: Update to 1.44.0 
- Bump PORTREVISION of dependent ports for shlib change

Changes:	https://github.com/grpc/grpc/releases
 2022-03-08 02:10:55 +08:00
Loïc Bartoletti
2d8f857316 devel/py-qt5, devel/py-sip: Update versions 
- Update sip to 6.5.1
- Update PyQt5 to 5.15.6
- Update PyQtChart, PyQtNetworkAuth and PyQtWebengine to 5.15.5
- Update PyQtSip to 12.9.1
- Update PyQtBuilder to 1.12.2
- Add ${_MAKE_JOBS} for pyqt.mk (reported by Tatsuki Makino)

PR:		261685
Exp-run by:	antoine
 2022-03-07 18:39:13 +01:00
Yuri Victorovich
af9abfe17c biology/py-loompy: Update 3.0.6 -> 3.0.7 
Reported by:	portscout
 2022-03-06 09:09:59 -08:00
Yuri Victorovich
ed361a72e0 biology/{,py-}libsedml: Update 2.0.27 -> 2.0.28 
Reported by:	portscout
 2022-03-05 18:15:32 -08:00
Thierry Thomas
ebbccfc73c biology/py-PySCeS: fix with Python ≠ 3.8 
PR:		262304
Approved by:	yuri (maintainer)
 2022-03-02 19:49:25 +01:00
Po-Chuan Hsieh
5412e0a5e4
biology/libsbml: Update WWW 2022-02-28 20:45:56 +08:00
Yuri Victorovich
40c0dcf270 biology/taxonkit: Update 0.9.0 -> 0.10.1 
Reported by:	portscout
 2022-02-27 10:35:41 -08:00
Jason W. Bacon
f46ddab3d6 biology/bio-mocha: Update bcftools submodule to 1.15 
Compatibility confirmed with upstream
 2022-02-26 09:04:10 -06:00
Jason W. Bacon
734d2c4df0 biology/bcftools: Update to 1.15 
Several small enhancements
Changes: https://github.com/samtools/bcftools/releases

Reported by:    portscout
 2022-02-26 09:04:10 -06:00
Jason W. Bacon
822ec7476b biology/samtools: Update to 1.15 
Several small enhancements and a few bug fixes
Changes: https://github.com/samtools/samtools/releases

Reported by:    portscout
 2022-02-26 09:04:10 -06:00
Jason W. Bacon
b3b13f54dc biology/htslib: Update to 1.15 
A few minor bug fixes and enhancements
No API changes affecting existing dependents

Reported by:    portscout
 2022-02-26 09:04:10 -06:00
Yuri Victorovich
7604abe7de biology/py-PySCeS: Update 1.0.0 -> 1.0.1 
Reported by:	portscout
 2022-02-25 11:35:50 -08:00
Joseph Mingrone
73b83478c1
biology/hyphy: Fix build with clang 13.0.0 
clang 13 complains about duplicate loop unrolling pragmas for clang and
CGG.  According to [1], clang supports #pragma GCC unroll with identical
semantics to #pragma clang loop unroll, so remove instances of #pragma
clang loop unroll and #pragma unroll when they appear with #pragma GCC
unroll for the same loop.

[1]
https://clang.llvm.org/docs/AttributeReference.html#pragma-unroll-pragma-nounroll

Sponsored by:	The FreeBSD Foundation
 2022-02-21 16:13:16 -04:00
Yuri Victorovich
9b5fb66610 biology/{,py-}libsedml: Update 2.0.26 -> 2.0.27 2022-02-16 16:27:20 -08:00
Jason W. Bacon
72923f58ba biology/py-dna-features-viewer: Add missing dependency 
py-packaging not mentioned in setup.py, but runtime errors thrown
without it.
 2022-02-12 09:12:39 -06:00
Fernando Apesteguía
8d34513c3f biology/pooler: update to 1.82 
ChangeLog: http://ssb22.user.srcf.net/pooler/#changes

PR:	261741
Reported by:	silas-freebsd@flatline.org.uk
 2022-02-10 15:23:48 +01:00
Jason W. Bacon
09167ae22b biology/freebayes: Update to 1.3.6 
Minor dependency updates, but mostly build system improvements
Changes:        https://github.com/freebayes/freebayes/tags

Reported by:    portscout
 2022-02-06 14:23:45 -06:00
Stefan Eßer
bdd2d4af96 Update CONFLICTS definitions in categories a* to c* 
Update the CONFLICTS definitions of ports in the following categories:

- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters

An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.

There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.

Approved by:	portmgr (implicit)
 2022-02-06 19:36:07 +01:00