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* biology/jalview: Fix build by using gradle-7.6.1 instead of gradle-8.0.1Yuri Victorovich2023-06-181-2/+2
| | | | | | The gradle upgrade seems to have broken jalview. Reported by: fallout
* biology/py-pysam: Update 0.20.0 → 0.21.0Yuri Victorovich2023-06-162-6/+5
| | | | Reported by: portscout
* biology/chip-seq: Metaport for ChIP-Seq analysisJason W. Bacon2023-06-144-0/+31
| | | | | | | Metaport to install tools for typical ChIP-Seq analysis, including QC, adapter trimming, alignment, and differential analysis. Presently identical to biology/atac-seq, but may diverge in the future.
* biology/biolibc: Update to 0.2.4.3Jason W. Bacon2023-06-102-4/+5
| | | | Add extern "C" to support use from C++ apps
* biology/peak-classifier: Update to 0.1.4.8Jason W. Bacon2023-06-102-6/+5
| | | | | Updates for libxtend API Minor fixes
* biology/fasda: Update to 0.1.3Jason W. Bacon2023-06-102-4/+4
| | | | | | | Improvements to test scripts and results analysis scripts Updates for libxtend API changes Code clean up Changes: outpaddling/libxtend/releases
* biology/biolibc-tools: Update to 0.1.4.6Jason W. Bacon2023-06-102-5/+5
| | | | | Improvements to deromanize Updates for libxtend API changes
* biology/abyss: Fix build with llvm15Muhammad Moinur Rahman2023-06-071-1/+7
| | | | Approved by: portmgr (blanket)
* biology/ncbi-toolkit: Fix build with llvm15Muhammad Moinur Rahman2023-06-061-1/+7
| | | | Approved by: portmgr (blanket)
* biology/gatk: Update 4.3.0.0 → 4.4.0.0Yuri Victorovich2023-06-042-8/+10
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* biology/fastp: Update to 0.23.4Jason W. Bacon2023-05-312-7/+4
| | | | | | | Fix regression in FASTQ reader Changes: https://github.com/OpenGene/fastp/releases Reported by: portscout
* biology/ncbi-blast+: Tag only for 64-bit architecturesJason W. Bacon2023-05-291-0/+3
| | | | | No longer builds on i386 or ppc Nobody does bioinformatics on 32-bit processors anymore
* biology/hyphy: Update to 2.5.51hfJoseph Mingrone2023-05-292-4/+4
| | | | | | FEL test still fails. See https://github.com/veg/hyphy/issues/1585. Sponsored by: The FreeBSD Foundation
* biology/libsedml: Fix build with libsbml 5.20.0Po-Chuan Hsieh2023-05-271-0/+11
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/libsedml/work/.build -- The CXX compiler identification is Clang 13.0.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working CXX compiler: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for BZ2_bzCompressInit in /usr/lib/libbz2.so -- Looking for BZ2_bzCompressInit in /usr/lib/libbz2.so - found -- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE) CMake Error at /usr/local/share/cmake/Modules/Internal/CheckSourceCompiles.cmake:51 (message): check_source_compiles: C: needs to be enabled before use. Call Stack (most recent call first): /usr/local/share/cmake/Modules/CheckCSourceCompiles.cmake:76 (cmake_check_source_compiles) CMakeModules/FindLIBXML.cmake:115 (CHECK_C_SOURCE_COMPILES) /usr/local/share/cmake/Modules/CMakeFindDependencyMacro.cmake:76 (find_package) /usr/local/lib/cmake/sbml-static-config.cmake:14 (find_dependency) /usr/local/share/cmake/Modules/FindLIBSBML.cmake:42 (find_package) CMakeLists.txt:338 (find_package) -- LIBXML_LIBXML_TEST = CMake Error at /usr/local/share/cmake/Modules/Internal/CheckSourceCompiles.cmake:51 (message): check_source_compiles: C: needs to be enabled before use. Call Stack (most recent call first): /usr/local/share/cmake/Modules/CheckCSourceCompiles.cmake:76 (cmake_check_source_compiles) CMakeModules/FindLIBXML.cmake:125 (CHECK_C_SOURCE_COMPILES) /usr/local/share/cmake/Modules/CMakeFindDependencyMacro.cmake:76 (find_package) /usr/local/lib/cmake/sbml-static-config.cmake:14 (find_dependency) /usr/local/share/cmake/Modules/FindLIBSBML.cmake:42 (find_package) CMakeLists.txt:338 (find_package) -- LIBXML_LIBXML_TEST2 = CMake Error at CMakeModules/FindLIBXML.cmake:132 (message): Unable to compile a test executable against LIBXML LIBXML_INCLUDE_DIR = /usr/local/include/libxml2 LIBXML_LIBRARY = /usr/local/lib/libxml2.so Call Stack (most recent call first): /usr/local/share/cmake/Modules/CMakeFindDependencyMacro.cmake:76 (find_package) /usr/local/lib/cmake/sbml-static-config.cmake:14 (find_dependency) /usr/local/share/cmake/Modules/FindLIBSBML.cmake:42 (find_package) CMakeLists.txt:338 (find_package) -- Configuring incomplete, errors occurred! *** Error code 1 Stop.
* biology/libcombine: Fix build with libsbml 5.20.0Po-Chuan Hsieh2023-05-271-0/+11
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | ===> Configuring for libcombine-0.2.20 ===> Performing out-of-source build /bin/mkdir -p /wrkdirs/usr/ports/biology/libcombine/work/.build -- The CXX compiler identification is Clang 13.0.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Check for working CXX compiler: /usr/local/libexec/ccache/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Looking for BZ2_bzCompressInit in /usr/lib/libbz2.so -- Looking for BZ2_bzCompressInit in /usr/lib/libbz2.so - found -- Could NOT find PkgConfig (missing: PKG_CONFIG_EXECUTABLE) CMake Error at /usr/local/share/cmake/Modules/Internal/CheckSourceCompiles.cmake:51 (message): check_source_compiles: C: needs to be enabled before use. Call Stack (most recent call first): /usr/local/share/cmake/Modules/CheckCSourceCompiles.cmake:76 (cmake_check_source_compiles) CMakeModules/FindLIBXML.cmake:115 (CHECK_C_SOURCE_COMPILES) /usr/local/share/cmake/Modules/CMakeFindDependencyMacro.cmake:76 (find_package) /usr/local/lib/cmake/sbml-static-config.cmake:14 (find_dependency) CMakeModules/FindLIBSBML.cmake:42 (find_package) CMakeLists.txt:308 (find_package) -- LIBXML_LIBXML_TEST = CMake Error at /usr/local/share/cmake/Modules/Internal/CheckSourceCompiles.cmake:51 (message): check_source_compiles: C: needs to be enabled before use. Call Stack (most recent call first): /usr/local/share/cmake/Modules/CheckCSourceCompiles.cmake:76 (cmake_check_source_compiles) CMakeModules/FindLIBXML.cmake:125 (CHECK_C_SOURCE_COMPILES) /usr/local/share/cmake/Modules/CMakeFindDependencyMacro.cmake:76 (find_package) /usr/local/lib/cmake/sbml-static-config.cmake:14 (find_dependency) CMakeModules/FindLIBSBML.cmake:42 (find_package) CMakeLists.txt:308 (find_package) -- LIBXML_LIBXML_TEST2 = CMake Error at CMakeModules/FindLIBXML.cmake:132 (message): Unable to compile a test executable against LIBXML LIBXML_INCLUDE_DIR = /usr/local/include/libxml2 LIBXML_LIBRARY = /usr/local/lib/libxml2.so Call Stack (most recent call first): /usr/local/share/cmake/Modules/CMakeFindDependencyMacro.cmake:76 (find_package) /usr/local/lib/cmake/sbml-static-config.cmake:14 (find_dependency) CMakeModules/FindLIBSBML.cmake:42 (find_package) CMakeLists.txt:308 (find_package) -- Configuring incomplete, errors occurred! *** Error code 1 Stop.
* biology/libsbml: Update to 5.20.0Po-Chuan Hsieh2023-05-275-566/+199
| | | | | | | | - Update MASTER_SITES - Update WWW - Sort PLIST Changes: https://github.com/sbmlteam/libsbml/releases
* biology/ncbi-blast+: Update to 2.14.0Jason W. Bacon2023-05-274-123/+827
| | | | | | A few bug fixes, enhancements, and performance improvements Changes: https://www.ncbi.nlm.nih.gov/books/NBK131777/
* biology/py-pysam: unbundle biology/htslibRobert Clausecker2023-05-251-2/+6
| | | | | | | | | This fixes the build on armv7 by picking up our custom fixed libhts over the bundled unfixed version. The CFLAGS workaround is now no longer required either. Approved by: yuri (maintainer) Differential Revision: https://reviews.freebsd.org/D40251
* biology/seqtk: Update to 1.4Jason W. Bacon2023-05-232-4/+4
| | | | | | | Several new subcommands Faster FASTX parsing Reported by: portscout
* biology/py-macs2: Update to 2.2.8Jason W. Bacon2023-05-222-5/+4
| | | | | | Adds support for python 3.11 Reported by: portscout
* biology/kmcp: Update 0.9.1 → 0.9.2Yuri Victorovich2023-05-222-7/+6
| | | | Reported by: portscout
* biology/gff2ps: drop maintainershipVinícius Zavam2023-05-211-1/+1
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* biology/biosoup: Update 0.10.0-2 → 0.11.0Yuri Victorovich2023-05-192-6/+4
| | | | Reported by: portscout
* */*: llvm15 build fixesMuhammad Moinur Rahman2023-05-172-2/+2
| | | | | | | llvm15 was also merged into 13.2-STABLE effective from OSVERSION 1302505. Fix the ports that failed to build with llvm15. Approved by: portmgr (blanket)
* biology/wise: Unbreak on HEADMuhammad Moinur Rahman2023-05-141-6/+16
| | | | | - Add LICENSE BSD3CLAUSE GPLv2 - Pet portclippy
* biology/fastp: Update to 0.23.3Jason W. Bacon2023-05-142-5/+6
| | | | | | | | Fix hang on bad input and a few other bugs Changes: https://github.com/OpenGene/fastp/releases Reported by: portscout
* biology/biosig: Unbreak on HEADMuhammad Moinur Rahman2023-05-121-1/+7
| | | | Approved by: portmgr (blanket)
* biology/py-multiqc: Update to 1.14Jason W. Bacon2023-05-123-28/+15
| | | | | | Numerous new features, enhancements and bug fixes Changes: https://github.com/ewels/MultiQC/releases
* biology/phyml: fix build on non-x86Robert Clausecker2023-05-084-2/+100
| | | | | | | | - only initialise x86-only fields on x86. - make code compatible with platforms where char is unsigned Obtained from: https://github.com/stephaneguindon/phyml/commit/9c55b683c875fb9923e7cb2a1092596f72040882 MFH: 2023Q2
* www/py-cachecontrol: Fix portPo-Chuan Hsieh2023-05-071-1/+1
| | | | | | | | | | | - Use lowercase PORTNAME - Fix WWW - Fix LICENSE - Fix FILECACHE and REDIS options: add missing RUN_DEPENDS - Bump PORTREVISION for package change PR: 266640 Approved by: maintainer (timeout, 3+ months)
* biology/minimap2: Update to 2.25Jason W. Bacon2023-04-293-10/+4
| | | | | | | | New feature to output sequences in secondary alignments Several minor enhancements and fixes Changes: https://github.com/lh3/minimap2/releases Reported by: portscout
* biology/bedtools: Update to 2.31.0Jason W. Bacon2023-04-292-4/+4
| | | | | | | | New summary tool Numerous minor fixes and enhancements Changes: https://github.com/arq5x/bedtools2/releases Reported by: portscout
* */*: bump all direct Boost cunsumersDima Panov2023-04-274-4/+4
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* biology/py-resdk: Update 16.0.0 → 17.0.0Yuri Victorovich2023-04-272-5/+4
| | | | Reported by: portscout
* audio/opus: bump consumers after update to 1.4Christian Weisgerber2023-04-256-5/+6
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* *: Bump PORTREVISIONs for math/mpc update to 1.3.1Gerald Pfeifer2023-04-2353-28/+53
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* devel/grpc: Update to 1.54.0 (should be part of ↵Po-Chuan Hsieh2023-04-191-1/+1
| | | | | | | | 8f17596cf5a75f2dca4b4c9f65ba02a53e1b2cd9) - Bump PORTREVISION of dependent ports for shlib change Changes: https://github.com/grpc/grpc/releases
* biology/hyphy: Update to 2.5.50Joseph Mingrone2023-04-192-4/+4
| | | | | | | This release fixes a bug when not using openmp. https://github.com/veg/hyphy/compare/2.5.49...2.5.50 Sponsored by: The FreeBSD Foundation
* biology/htslib: fix build on armv7Robert Clausecker2023-04-183-0/+25
| | | | | | | | | | This project includes some SIMD-enhanced functions for ARM NEON. Unfortunately the code uses a bunch of intrinsics only available on aarch64. Disable the use of NEON on armv6 and armv7 to fix the build on these platforms. See also: https://github.com/samtools/htslib/issues/1603 Approved by: portmgr (build fix blanket)
* biology/py-libsedml: Allow build with swig 4.1.0+Po-Chuan Hsieh2023-04-181-1/+12
| | | | | PR: 270720 Obtained from: https://github.com/fbergmann/libSEDML/commit/f0a9ee974826a3ef651ecb2553b10ea47f652bc5
* biology/py-libnuml: Allow build with swig 4.1.0+Po-Chuan Hsieh2023-04-181-1/+10
| | | | | PR: 270720 Obtained from: https://github.com/NuML/NuML/commit/b8766a6bcc3083a5d4f5aa0d166d66d8c80f1345
* biology/taxonkit: Update 0.14.1 → 0.14.2Yuri Victorovich2023-04-152-7/+6
| | | | Reported by: portscout
* all: Bump PORTREVISION after lang/go{119,120} updateDmitri Goutnik2023-04-085-5/+5
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* biology/libsbml: Update WWW and clean up pkg-descrPo-Chuan Hsieh2023-04-052-4/+3
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* USE_PYTHON=pep517: bump PORTREVISIONAntoine Brodin2023-04-041-0/+1
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* */*: Refactor java/openjdk7 removalMuhammad Moinur Rahman2023-04-042-2/+2
| | | | | | | | | | | | | | | - java/openjdk7* has been removed from the tree since 2022-09-03 however the relevant codebases in bsd.java.mk has not been removed and the consumers has also not been updated to use the next jdk version. This commit updates all relevant consumers to use JAVA_VERSION=8 instead of JAVA_VERSION=1.7 - Since the introduction of jdk version 18 it looks like similar with jdk version 8(java version string 1.8). This is prone to error as it looks similar and is only seperated by a '.'. Remove using JAVA_VERSION with dotted fomat of java version string and update all consumers to utilize version 8 instead of 1.8. Approved by: portmgr (blanket)
* biology/py-pybigwig: Update to 0.3.21Jason W. Bacon2023-04-012-4/+4
| | | | | | No relevant changes, just an upstream wheel fix. Reported by: portscout
* */*: Sunset 12.3-RELEASE from ports tree12.3-eolMuhammad Moinur Rahman2023-03-301-10/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Mk/bsd.port.mk: mark FreeBSD 12.3 as unsupported. - Mk/Uses/cabal.mk: Remove the text-2 workaround for 12.3-RELEASE - biology/wfa2-lib: remove obsolete patch - databases/mongodb60: remove IGNORE for EOL FreeBSD 12.3 - devel/concurrencpp: remove workaround for EOL FreeBSD 12.3 - devel/electron22: remove IGNORE for EOL FreeBSD 12.3 - devel/malloy: this should build fine on 12.4-RELEASE - devel/qcoro: remove BROKEN for EOL FreeBSD 12.3 - devel/root: remove workaround for EOL FreeBSD 12.3 - editors/imhex: remove IGNORE for EOL FreeBSD 12.3 - emulators/ppsspp: remove workaround for EOL FreeBSD 12.3 - emulators/rpcs3: remove workaround for EOL FreeBSD 12.3 - emulators/yuzu: remove workaround for EOL 12.3-RELEASE - games/aquaria: remove support for EOL FreeBSD 12.3 - games/punchy: remove workaround for EOL FreeBSD 12.3 - graphics/cxxplot: remove support for EOL FreeBSD 12.3 - lang/gcc11*: bump a __FreeBSD_version in libphobos to 1204000 - lang/rust: untangle OSVERSION logic a bit - misc/mbuffer: remove workaround for EOL FreeBSD 12.3 for aarch64 - sysutils/libdisplay-info: remove workaround for EOL FreeBSD 12.3 - www/*chromium: remove IGNORE for EOL FreeBSD 12.3 - x11/hyprpaper: remove workaround for expired FreeBSD 12.3 - x11-wm/labwc: remove workaround for EOL FreeBSD 12.3 - x11-wm/kwinft: remove workaround for EOL FreeBSD 12.3 - www/iridium: remove IGNORE for EOL FreeBSD 12.3 Differential Revision: https://reviews.freebsd.org/D38664
* biology/kmcp: fix build on i386 and riscv64Robert Clausecker2023-03-242-0/+20
| | | | | | | | | - fix an issue with wrong copy-editing in a fork of one of my Go packages - fix an issue with wrong build constraints Sponsored by: Berliner Linux User Group e.V. Approved by: portmgr (build fix blanket)
* biology/hyphy: Update to 2.5.49Joseph Mingrone2023-03-242-5/+5
| | | | Sponsored by: The FreeBSD Foundation
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