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* cleanup: remove transitive py27 deprecation (www/qt5-webengine)Rene Ladan2022-01-302-6/+0
| | | | (cherry picked from commit 48d98ef9181e828b575f37e1841ad53e5def5987)
* biology/minimap2: Update to 2.24Jason W. Bacon2021-12-312-5/+4
| | | | | | Fix chaining algorithm issue resulting in poorly aligned regions Reported by: portscout
* biology/fastp: Update to 0.23.2Jason W. Bacon2021-12-302-4/+4
| | | | Interleaved input bug fix
* biology/py-resdk: Update 13.7.0 -> 13.8.0Yuri Victorovich2021-12-302-4/+4
| | | | Reported by: portscout
* devel/grpc: Update to 1.42.0Po-Chuan Hsieh2021-12-211-1/+1
| | | | Changes: https://github.com/grpc/grpc/releases
* bio-mocha: Build plugin against bcftools 1.14, the current portJason W. Bacon2021-12-212-5/+7
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* biology/py-bx-python: Update 0.8.11-6 -> 0.8.13Yuri Victorovich2021-12-212-10/+5
| | | | Reported by: portscout
* biology/canu: fix CATEGORIESAntoine Brodin2021-12-201-1/+1
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* biology/py-pysam: Update 0.16.0.1 -> 0.18.0Wen Heping2021-12-202-4/+4
| | | | PR: 260556
* biology/canu: Update to 2.2Jason W. Bacon2021-12-1911-13/+204
| | | | | | | | | FreeBSD port: Add support for aarch64 and powerpc64 using simde Not yet supported upstream Several upstream bug fixes and minor enhancements since 2.1 Changes: https://github.com/marbl/canu/tags
* biology/seqtk: Update to 1.3Jason W. Bacon2021-12-183-17/+29
| | | | | | A few minor fixes and enhancements Changes: https://github.com/lh3/seqtk/tags
* biology/bcftools: Update to 1.14Jason W. Bacon2021-12-182-4/+4
| | | | | | A few minor enhancements and bug fixes Changes: https://github.com/samtools/bcftools/tags
* biology/samtools: Update to 1.14Jason W. Bacon2021-12-183-4/+5
| | | | | | Several enhancements and minor bug fixes Changes: https://github.com/samtools/samtools/tags
* biology/htslib: Update to 1.14Jason W. Bacon2021-12-182-4/+4
| | | | | | Several minor enhancements and fixes Changes: https://github.com/samtools/htslib/tags
* biology/freebayes: enable on riscv64Piotr Kubaj2021-12-171-1/+0
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* biology/vcflib: unbreak on riscv64Piotr Kubaj2021-12-161-3/+0
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* biology/hisat2: enable on riscv64Piotr Kubaj2021-12-161-1/+1
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* biology/bowtie: enable on riscv64Piotr Kubaj2021-12-151-2/+2
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* biology/vcf2hap: Update to 0.1.4Jason W. Bacon2021-12-142-5/+5
| | | | | Updates for evolving libxtend and biolibc APIs Add --version flag
* biology/vcf-split: Update to 0.1.3.3Jason W. Bacon2021-12-142-5/+6
| | | | | | | Transfer header from multi-sample input Updates for evolving libxtend and biolibc APIs Add --version flag Numerous minor fixes and enhancements
* biology/peak-classifier: Update to 0.1.2Jason W. Bacon2021-12-142-5/+4
| | | | | Mainly updates for evolving libxtend and biolibc APIs A few minor fixes and enhancements
* biology/biolibc-tools: Update to 0.1.1Jason W. Bacon2021-12-143-12/+25
| | | | | | | | | | Make all programs subcommands of "blt" Several new commands Updates for evolving libxtend and biolibc APIs Add --version flag Numerous minor fixes and enhancements Changes: https://github.com/auerlab/biolibc-tools/releases/tag/0.1.1
* biology/ad2vcf: Update to 0.1.4Jason W. Bacon2021-12-142-5/+5
| | | | | | | | | Updates for evolving libxtend and biolibc APIs Add --version flag Filter out unused SAM fields on input Numerous other minor fixes and enhancements Changes: https://github.com/auerlab/ad2vcf/releases/tag/0.1.4
* biology/biolibc: Update to 0.2.1Jason W. Bacon2021-12-143-183/+8
| | | | | | | | | | Add orf.c with start/stop codon locators Standardize BED and GFF APIs Implement VCF input filtering Eliminate mutator macros mirroring mutator functions Numerous minor bug fixes and enhancements Changes: https://github.com/auerlab/biolibc/releases/tag/0.2.1
* biology/bowtie: Update to 1.3.1Jason W. Bacon2021-12-146-80/+34
| | | | | | | | | Also adds support for aarch64 and powerpc64* Changes: https://github.com/BenLangmead/bowtie/tags PR: 260389 Reported by: pkubaj
* devel/automake: update to 1.16.5Tijl Coosemans2021-12-122-2/+29
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* biology/seaview: Update version 5.0.4=>5.0.5Muhammad Moinur Rahman2021-12-063-77/+4
| | | | Relnotes: http://doua.prabi.fr/software/seaview_data/CHANGES
* biology/libgff: GFF/GTF parsing library based on GCLibJason W. Bacon2021-12-055-0/+45
| | | | | | | | | | | | This is an attempt to perform a simple "libraryfication" of the GFF/GTF parsing code that is used in GFFRead codebase. There are not many (any?) relatively lightweight GTF/GFF parsers exposing a C++ interface, and the goal of this library is to provide this functionality without the necessity of drawing in a heavy-weight dependency like SeqAn. Note: This library draws directly from the code in GFFRead and GCLib, and exists primarily to remove functionality (and hence code) that is unnecessary for our downstream purposes. In the future, it may be appropriate to just replace this library wholesale with GCLib.
* biology/minimap2: Unbreak on i386 by resotring -msse flagsJason W. Bacon2021-12-032-18/+3
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* biology/bio-mocha: bcftools plugin for mosaic chromosomal alterationsJason W. Bacon2021-12-039-0/+613
| | | | | | | | | MoChA is a bcftools plugin released under the MIT license for mosaic chromosomal alteration detection and analysis from DNA microarray or whole genome sequence data. It can be used both with Illumina and Affymetrix data. It can also be used for detection of germline copy number variants. Data can be prepared in usable file formats using the gtc2vcf plugin.
* biology/taxonkit: Update 0.8.0 -> 0.9.0Yuri Victorovich2021-12-022-6/+6
| | | | Reported by: portscout
* biology/bwa: don't use GCC on powerpc64lePiotr Kubaj2021-12-011-3/+0
| | | | Now that the port uses simde, it builds fine without gcc's translation.
* biology/biostar-tools: Allow package build on non-amd64 systemsJason W. Bacon2021-12-012-4/+10
| | | | | | Only sra-tools is still non-portable, but it will take some time to add support for other architectures. In the meantime, allow aarch64 and powerpc64 users to have a biostar-tools package.
* biology/bwa: Unbreak on most non-x86 platforms using simdeJason W. Bacon2021-12-012-7/+17
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* biology/minimap2: Update to 2.23Jason W. Bacon2021-11-305-71/+103
| | | | | | | Also switch to SIMDE Makefile to support non-x86 platforms Changes: https://github.com/lh3/minimap2/releases/tag/v2.23 Reported by: portscout
* biology/hisat2: Add support for powerpc64* and aarch64Jason W. Bacon2021-11-285-4/+70
| | | | | | Minor patches to utilize simde to emulate SSE (from Debian package) Add -fsigned-char since clang defaults to unsigned on aarch64 Remove -DPOPCNT_CAPABILITY (not truly safe even on amd64)
* biology/hisat2: Remove patch causing quality scores of "-0"Jason W. Bacon2021-11-272-11/+1
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* biology/hisat2: Update to 2.2.1Jason W. Bacon2021-11-266-480/+99
| | | | Changes: https://github.com/DaehwanKimLab/hisat2/tags
* biology/star: Update to 2.7.9aJason W. Bacon2021-11-268-35/+162
| | | | | | Also unbundle htslib Changes: https://github.com/alexdobin/STAR/releases/tag/2.7.9a
* */*: Remove redundant '-*' from CONFLICTS definitionsStefan Eßer2021-11-251-1/+1
| | | | | | | | | The conflict checks compare the patterns first against the package names without version (as reported by "pkg query "%n"), then - if there was no match - agsinst the full package names including the version (as reported by "pkg query "%n-%v"). Approved by: portmgr (blanket)
* biology/rubygem-bio-shell: Update to 1.0.1Po-Chuan Hsieh2021-11-212-4/+4
| | | | Changes: https://github.com/bioruby/bioruby-shell/commits/master
* biology/cd-hit: fix build on armv7Piotr Kubaj2021-11-211-1/+1
| | | | Same issue as on powerpc.
* biology/py-resdk: Update 13.6.0 -> 13.7.0Yuri Victorovich2021-11-182-4/+4
| | | | Reported by: portscout
* biology/hyphy: Update to 2.5.33Joseph Mingrone2021-11-172-4/+4
| | | | https://github.com/veg/hyphy/releases/tag/2.5.33
* biology/seqkit: Update 2.0.1 -> 2.1.0Yuri Victorovich2021-11-162-6/+6
| | | | Reported by: portscout
* biology/hhsuite: fix packaging on powerpcPiotr Kubaj2021-11-162-4/+10
| | | | | | | | | pkg-static: Unable to access file /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhalign_omp:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhblits_ca3m:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhblits_omp:No such file or directory pkg-static: Unable to access file /wrkdirs/usr/ports/biology/hhsuite/work/stage/usr/local/bin/hhsearch_omp:No such file or directory powerpc doesn't have LLVM with libomp.
* biology/seqan3: Update 3.0.3 -> 3.1.0Yuri Victorovich2021-11-153-169/+36
| | | | Reported by: portscout
* biology/hyphy: enable on armv7Piotr Kubaj2021-11-121-1/+1
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* biology/diamond: Update to 2.0.13Joseph Mingrone2021-11-112-4/+4
| | | | | This update fixes a bug that caused invalid bit scores in frameshift alignment mode.
* biostar-tools: Add gffread to metaport depsJason W. Bacon2021-11-102-3/+4
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