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4014 Commits

Author SHA1 Message Date
Yuri Victorovich
c1ef3af576 biology/btllib: update 1.7.2 → 1.7.3 
Reported by:	portscout
 2024-07-27 13:19:18 -07:00
Jason W. Bacon
771236eb8e biology/kallisto: Update to 0.51.0,1 
Add support for long reads to kallisto bus and kallisto quant-tcc
Changes: https://github.com/pachterlab/kallisto/releases

Reported by:    portscout
 2024-07-27 07:02:57 -05:00
Yuri Victorovich
63806c7d1f biology/py-mrcfile: update 1.5.2 → 1.5.3 
Reported by:	portscout
 2024-07-26 01:57:55 -07:00
Neel Chauhan
18b2a58890 biology/p5-TrimGalore: Update to 0.6.10 2024-07-23 11:01:28 -04:00
Yuri Victorovich
46f1e26693 biology/py-pyrodigal: update 3.5.0 → 3.5.1 
Reported by:	portscout
 2024-07-22 17:34:23 -07:00
Yuri Victorovich
01f227d608 biology/abyss: update 2.3.7 → 2.3.8 
Reported by:	portscout
 2024-07-22 17:34:22 -07:00
Yuri Victorovich
ee70f36f9b biology/py-mrcfile: update 1.5.1 → 1.5.2 
Reported by:	portscout
 2024-07-22 17:34:22 -07:00
Jason W. Bacon
f84c63104e biology/minimap2: Add NOT_FOR_ARCHS for most 32-bit processors 
Upstream supports specific architectures, mainly 64-bit and ARM Neon
 2024-07-20 14:55:08 -05:00
Tijl Coosemans
c8eeb158e4 devel/automake: Update to 1.17 
biology/libneurosim: Fix use of libltdl.

dns/ddclient: Take out -Werror.

lang/sdcc:
- Patching ARCH is no longer needed.  Remove it because it touched some
  configure.ac files and that causes other autotools files to appear
  out-of-date.
- Run autoreconf in WRKSRC/device/lib/pic14 because aclocal.m4 and
  config.h.in appear out-of-date.

net/rpki-client: Patch Makefile.in instead of Makefile.am to avoid
autotools.

sysutils/genimage: Run configure with --disable-silent-rules because
upstream changed the default to silent and when silent rules are
enabled it also runs make with --no-print-directory which is a gmake
flag.  Patch Makefile.am so it uses --no-print-directory depending on
the actual verbosity instead of the default.

PR:		280277
Exp-run by:	antoine
 2024-07-20 13:27:02 +02:00
Yuri Victorovich
9e9db724e2 biology/gatk: Fix fetch 2024-07-20 01:36:53 -07:00
Yuri Victorovich
38f9715deb biology/py-pyrodigal: update 3.4.1 → 3.5.0 
Reported by:	portscout
 2024-07-18 01:22:46 -07:00
Yuri Victorovich
c3b8a41d7f biology/gatk: Fix fetch 
Reported by:	fallout
 2024-07-14 09:32:42 -07:00
Yuri Victorovich
c4faabf62b biology/gatk: Prevent execution of git hooks from $DISTDIR during fetch 2024-07-13 11:35:06 -07:00
Yuri Victorovich
44ec9c8c3f biology/py-biom-format: update 2.1.10 → 2.1.16 
PR:	279854
Approved by:	Joseph Mingrone <jrm@freebsd.org> (maintainer)
 2024-07-13 11:06:57 -07:00
Yuri Victorovich
e9af3287f7 biology/py-scikit-bio: update 0.6.1 → 0.6.2 
Reported by:	portscout
 2024-07-12 22:17:53 -07:00
Yuri Victorovich
40e4fb82e9 biology/py-resdk: update 21.1.0 → 21.2.0 
Reported by:	portscout
 2024-07-12 01:58:00 -07:00
Yuri Victorovich
0700adfcc5 biology/py-mrcfile: update 1.5.0 → 1.5.1 
Reported by:	portscout
 2024-07-12 01:57:59 -07:00
Yuri Victorovich
290983fbb4 biology/gatk: update 4.5.0.0 → 4.6.0.0 2024-07-11 20:51:21 -07:00
Piotr Kubaj
b5a4f7a9a4 biology/migrate: fix build on !x86 2024-07-09 12:04:31 +02:00
Jason W. Bacon
84a6e7ec36 biology/gcta: Unbreak fetch 
Fix mysterious distinfo corruption
 2024-07-08 17:04:44 -05:00
Po-Chuan Hsieh
1a80ec7c22
devel/py-pyyaml: Move devel/py-yaml to devel/py-pyyaml 
- Bump PORTREVISION of dependent ports for dependency change
 2024-07-07 16:05:33 +08:00
Yuri Victorovich
1df121116e biology/ncbi-cxx-toolkit: update 28.0.5 → 28.0.6 
Reported by:	portscout
 2024-07-06 18:27:07 -07:00
Yuri Victorovich
74f010bc95 biology/taxonkit: update 0.16.0 → 0.17.0 
Reported by:	portscout
 2024-07-04 09:32:16 -07:00
Ganael LAPLANCHE
149e2101c3 devel/onetbb: Update to 2021.13.0 
and bump dependent ports' revisions.

Release notes:	https://github.com/oneapi-src/oneTBB/blob/v2021.13.0/RELEASE_NOTES.md
 2024-07-04 13:39:44 +02:00
Wen Heping
b6abf92309 biology/py-dnaio: Update to 1.2.1 
Take maintainership
 2024-07-04 09:15:39 +00:00
Ashish SHUKLA
c4b51c2028
all: Bump after lang/go121 update 2024-07-03 08:29:54 +00:00
Joseph Mingrone
6313182221
biology/iqtree: Update to 2.3.5 
Release Notes:	https://github.com/iqtree/iqtree2/releases/tag/v2.3.5
Sponsored by:	The FreeBSD Foundation
 2024-07-01 18:28:31 -03:00
Rene Ladan
19d68720f1 all: drop support for FreeBSD 13.2 which reached EOL today 
Thanks again to jbeich for noticing various things I overlooked.

Reviewed by:	acm, ashish, eduardo, ehaupt, eugen, jbeich, martymac, mat, nobukata, sunpoet, tagattie, yuri, arrowd, kde
Differential Revision:	https://reviews.freebsd.org/D45141
 2024-07-01 22:27:23 +02:00
Jason E. Hale
ad593a9d4d */*: Add ${PY_SETUPTOOLS} to BUILD_DEPENDS 
Fix build when setuptools is removed from RUN_DEPENDS in
Mk/Uses/python.mk.

PR:		270510
Approved by:	portmgr (blanket)
 2024-06-29 01:02:34 -04:00
Thierry Thomas
e2cd1133e6 */*: bump PORTREVISION after the upgrade to OpenBLAS 2024-06-21 19:49:24 +02:00
Joseph Mingrone
175e67eaf3
biology/hyphy: Update to 2.5.62 
Commit log:	https://github.com/veg/hyphy/compare/2.5.61...2.5.62
Sponsored by:	The FreeBSD Foundation
 2024-06-21 13:58:09 -03:00
Philippe Audeoud
62058b84ea biology/py-cutadapt: update to 4.9 
changelog: https://cutadapt.readthedocs.io/en/stable/changes.html#v4-9-2024-06-19
 2024-06-20 10:38:00 +02:00
Yuri Victorovich
45967dddbb biology/py-scikit-bio: update 0.6.0 → 0.6.1 
Reported by:	portscout
 2024-06-19 02:56:10 -07:00
Daniel Engberg
fee36575d6
biology/libsbml: Fix build with libxml2 2.12.0+ 
PR:		279752
Obtained from:	a3e217851f
 2024-06-18 12:05:09 +08:00
Yuri Victorovich
324d0273f5 biology/py-gffutils: update 0.11.1 → 0.13 2024-06-16 18:20:35 -07:00
Piotr Kubaj
90c6e11540 biology/phyml: fix build on non-amd64 
cc: error: unsupported option '-msse3' for target 'powerpc64-unknown-freebsd14.1'
 2024-06-16 17:25:18 +02:00
Ashish SHUKLA
746fa696a1
all: Bump after lang/go121 update 
MFH:		2024Q2
 2024-06-15 09:52:17 +00:00
Älven
2a46a41f8c biology/unikmer: update 0.19.1 → 0.20.0 
PR:	279674
 2024-06-11 10:11:41 -07:00
Ruslan Makhmatkhanov
de4b547a33 biology/py-pywgsim: fix build 
cython dependency not available at post-patch stage. Use post-configure instead

Approved by:	portmgr (blanket approval)
 2024-06-07 11:11:35 +03:00
Yuri Victorovich
15552b1293 biology/ncbi-cxx-toolkit: update 28.0.4 → 28.0.5 
Reported by:	portscout
 2024-06-06 01:49:02 -07:00
Ruslan Makhmatkhanov
91e7916b1c biology/py-pywgsim: unbreak with python3.11 
make it recreate the source with newer cython

PR:		275494
Approved by:	portmgr (blanket approval)
 2024-06-04 14:55:31 +03:00
Antoine Brodin
f1e51f12a7 biology/py-pywgsim: unbreak bulk -a 2024-06-03 12:18:08 +00:00
Jason W. Bacon
155267db53 biology/py-pywgsim: Limit to python 3.10 
Nontrivial changes needed for python 3.11
Abandoned upstream

Reported by:    pkg-fallout
 2024-06-03 06:41:44 -05:00
Jason W. Bacon
b873231515 biology/biostar-tools: Update to 1.11 
Drop abandonware py-pywgsim dep

Reported by:    pkg-fallout
 2024-06-03 06:38:30 -05:00
Yuri Victorovich
52d2c144f4 biology/metaeuk: update 6 → 7 
Reported by:	portscout
 2024-06-01 01:10:52 -07:00
Jason W. Bacon
3bf602d2a7 biology/gcta: Unbreak build on 14.x aarch64 
Missing #include <cstdint> in a few files

Reported by:    pkg-fallout
 2024-05-28 16:26:06 -05:00
Jason W. Bacon
b1e94269b6 biology/stacks: Unbreak build on aarch64 
ARM clang is intolerant of implicit demotions in initializers

Reported by:    pkg-fallout
 2024-05-28 16:17:25 -05:00
Jason W. Bacon
859980f9d8 biology/minimap2: Unbreak build on aarch64 
Remove unsupports -msse flags

Reported by:    pkg-fallout
 2024-05-28 16:06:42 -05:00
Philippe Audeoud
81c4dbffdc biology/py-cutadapt: update to 4.8 
While here, take maintainership
 2024-05-28 13:28:21 +02:00
Yuri Victorovich
9997daa479 biology/py-PySCeS: update 1.1.1 → 1.2.1 
Reported by:	portscout
 2024-05-26 14:57:06 -07:00