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* biology/taxonkit: Update 0.11.1 -> 0.12.0Yuri Victorovich2022-06-092-7/+6
| | | | Reported by: portscout
* biology/{,py-}libsedml: Update 2.0.31 -> 2.0.32Yuri Victorovich2022-06-095-11/+13
| | | | Reported by: portscout
* */*: Bump port revisons after lang/go{117,118} updateDmitri Goutnik2022-06-074-1/+4
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* biology/py-resdk: Update 14.1.0 -> 15.0.0Yuri Victorovich2022-06-072-4/+6
| | | | Reported by: portscout
* biology/py-gffutils: Update 0.10.1 -> 0.11.0Yuri Victorovich2022-06-072-4/+4
| | | | Reported by: portscout
* */*: Repair after switching to versioned Go portsDmitri Goutnik2022-06-061-1/+1
| | | | | | | | | | - 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
* biology/py-scikit-bio: Broken on aarch64Yuri Victorovich2022-06-031-0/+2
| | | | Reported by: fallout
* biology/py-pysam: Update 0.19.0 -> 0.19.1Yuri Victorovich2022-05-312-4/+4
| | | | Reported by: portscout
* biology/hyphy: Update to 2.5.39Joseph Mingrone2022-05-272-4/+4
| | | | | | https://github.com/veg/hyphy/releases/tag/2.5.39hf1 Sponsored by: The FreeBSD Foundation
* biology/gatk: Use Java 17 instead of EOLed Java 12Yuri Victorovich2022-05-242-4/+5
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* cleanup: remove expired versions of OpenJDK (12 through 16)Rene Ladan2022-05-241-1/+1
| | | | | | | | | | | | | | | | | | 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
* biology/gatk: Update 4.2.6.0 -> 4.2.6.1Yuri Victorovich2022-05-232-7/+10
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* devel/boost-all: bump all library consumers after boost upgradeDima Panov2022-05-226-4/+6
| | | | PR: 246106
* biology/cufflinks: mark as BROKEN after recent boost upgradeDima Panov2022-05-221-0/+2
| | | | PR: 246106
* biology/py-PySCeS: Update 1.0.1 -> 1.0.2Yuri Victorovich2022-05-202-4/+4
| | | | Reported by: portscout
* biology/taxonkit: Update 0.11.0 -> 0.11.1Yuri Victorovich2022-05-202-6/+6
| | | | Reported by: portscout
* biology/mothur: Update 1.47.0 -> 1.48.0Yuri Victorovich2022-05-202-5/+5
| | | | Reported by: portscout
* biology/biosig: Update 2.4.0 -> 2.4.1Yuri Victorovich2022-05-163-5/+6
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* biology/taxonkit: Update 0.10.1 -> 0.11.0Yuri Victorovich2022-05-162-7/+6
| | | | Reported by: portscout
* devel/cmake: Update to 3.23.0Loïc Bartoletti2022-05-161-1/+1
| | | | | | | | | | | 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
* devel/grpc: Update to 1.46.0Po-Chuan Hsieh2022-05-131-1/+1
| | | | | | - Bump PORTREVISION of dependent ports for shlib change Changes: https://github.com/grpc/grpc/releases
* devel/libffi: Bump deps PORTREVISION for shlib changeKevin Bowling2022-05-091-0/+1
| | | | | PR: 263764 Reported by: VVD <vvd@unislabs.com>
* biology/py-dna-features-viewer: Update to 3.1.1Jason W. Bacon2022-05-082-5/+4
| | | | | | | | python 3.9 compatibility Changes: https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer/tags Reported by: portscout
* biology/checkm: Update 1.1.11 -> 1.2.0Yuri Victorovich2022-05-012-8/+8
| | | | Reported by: portscout
* biology/py-mrcfile: New port: MRC file I/O library which is used in ↵Yuri Victorovich2022-05-014-0/+28
| | | | structural biology
* biology/py-pysam: Update 0.18.0 -> 0.19.0Yuri Victorovich2022-04-272-4/+4
| | | | Reported by: portscout
* biology/py-resdk: Update 14.0.0 -> 14.1.0Yuri Victorovich2022-04-272-4/+4
| | | | Reported by: portscout
* biology/pooler: use openmp only when omp.h is presentPiotr Kubaj2022-04-271-5/+2
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* biology/ncbi-blast+: check for omp.h on all architecturesPiotr Kubaj2022-04-271-4/+4
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* biology/cd-hit: check for omp.h on all architecturesPiotr Kubaj2022-04-271-3/+1
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* biology/hhsuite: check for omp.h on all architecturesPiotr Kubaj2022-04-271-6/+6
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* biology/fasttree: check for omp.h on all architecturesPiotr Kubaj2022-04-271-5/+1
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* biology/unikmer: Update 0.18.8 -> 0.19.0Yuri Victorovich2022-04-262-7/+6
| | | | Reported by: portscout
* biology/checkm: Update 1.1.10 -> 1.1.11Yuri Victorovich2022-04-252-4/+4
| | | | Reported by: portscout
* biology/seqan-apps: remove obsolete USE_GCCPiotr Kubaj2022-04-251-5/+1
| | | | Instead use USES=compiler.
* biology/hyphy: Update to 2.5.38Joseph Mingrone2022-04-245-231/+11
| | | | | | Upstream changes: https://github.com/veg/hyphy/compare/2.5.36...2.5.38 Sponsored by: The FreeBSD Foundation
* biology/diamond: Update to 2.0.15Joseph Mingrone2022-04-242-4/+4
| | | | | | https://github.com/bbuchfink/diamond/releases/tag/v2.0.15 Sponsored by: The FreeBSD Foundation
* biology/{,py-}libnuml: Update 1.1.5 -> 1.1.6Yuri Victorovich2022-04-245-10/+9
| | | | Reported by: portscout
* biology/{,py-}libsedml: Update 2.0.30 -> 2.0.31Yuri Victorovich2022-04-225-10/+9
| | | | Reported by: portscout
* biology/checkm: Update 1.1.9 -> 1.1.10Yuri Victorovich2022-04-222-4/+4
| | | | Reported by: portscout
* biology/hhsuite: drop HAVE_POWER8 on powerpc64Piotr Kubaj2022-04-211-1/+2
| | | | powerpc64 uses PPC970 as a baseline.
* biology/py-scikit-bio: drop unnecessary USE_GCC on powerpc64Piotr Kubaj2022-04-211-4/+1
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* biology/bolt-lmm: remove unnecessary CFLAGS_powerpc64Piotr Kubaj2022-04-211-1/+0
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* biology/seqkit: Update 2.1.0 -> 2.2.0Yuri Victorovich2022-04-202-7/+6
| | | | Reported by: portscout
* biology/py-scikit-bio: build with clang on powerpc64lePiotr Kubaj2022-04-191-1/+2
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* biology/bolt-lmm: remove unnecessary flags for powerpc64lePiotr Kubaj2022-04-171-1/+0
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* biology/checkm: Update 1.1.8 -> 1.1.9Yuri Victorovich2022-04-152-4/+4
| | | | Reported by: portscout
* biology/py-scikit-bio: Update 0.5.6 -> 0.5.7Yuri Victorovich2022-04-152-7/+8
| | | | Reported by: portscout
* biology/checkm: Update 1.0.18 -> 1.1.8Yuri Victorovich2022-04-123-656/+8
| | | | Reported by: portscout
* biology/gatk: Update 4.2.0.0 -> 4.2.6.0Yuri Victorovich2022-04-102-8/+8
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