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* biology/fasttree: fix build on armv7Piotr Kubaj2021-06-151-2/+1
| | | | Same issue as with powerpc.
* biology/peak-classifier: Classify peaks based on GFF featuresJason W. Bacon2021-06-145-0/+45
| | | | | | | | | | Classify ChIP/ATAC-Seq peaks based on features provided in a GFF Peaks are provided in a BED file sorted by chromosome and position. The GFF must be sorted by chromosome and position, with gene-level features separated by ### tags and each gene organized into subfeatures such as transcripts and exons. This is the default for common data sources.
* math/lapack: +math/blas et al., upgrade to 3.9.1Thierry Thomas2021-06-132-1/+13
| | | | | | | | | | | | | | | | | - Upgrade math/blas, math/cblas, math/lapack, math/lapacke and math/xlapack to 3.9.1; Latest release notes at <http://www.netlib.org/lapack/lapack-3.9.1.html> - Chase this upgrade in biology/treekin; - Add a test target; - Remove a conflict with math/openblas (PR 244296); - Fix the build with Gcc10 (PR 247485). PR: 247542 Approved by: expr-run by antoine@
* biology/vcf2hap: Remove comment used to silence portlintJason W. Bacon2021-06-111-2/+0
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* biology/ad2vcf: Remove comment used to silence portlintJason W. Bacon2021-06-111-2/+0
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* biology/biolibc: Remove comment used to silence portlintJason W. Bacon2021-06-111-2/+0
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* biology/vcf-split: Update to 0.1.2Jason W. Bacon2021-06-112-5/+5
| | | | | | Updates for new biolibc API Changes: https://github.com/auerlab/vcf-split/releases
* biology/vcf2hap: Update to 0.1.3Jason W. Bacon2021-06-113-7/+11
| | | | | | Updates for new biolibc API Changes: https://github.com/auerlab/vcf2hap/releases
* biology/ad2vcf: Update to 0.1.3Jason W. Bacon2021-06-113-9/+9
| | | | | | Updates for new biolibc API Changes: https://github.com/auerlab/ad2vcf/releases
* biology/biolibc: Update to 0.1.3Jason W. Bacon2021-06-113-9/+42
| | | | Changes: https://github.com/auerlab/biolibc/releases
* biology/fasttree: fix build on powerpcPiotr Kubaj2021-06-101-0/+6
| | | | | LLVM on powerpc doesn't have libomp. Same issue happens on armv6 and armv7 but someone has to test whether doing the same for those architectures is enough.
* biology/cd-hit: fix build on powerpcPiotr Kubaj2021-06-101-0/+6
| | | | | LLVM on powerpc doesn't have libomp: cdhit-common.c++:36:9: fatal error: 'omp.h' file not found
* biology/hyphy: Update to 2.5.31Joseph Mingrone2021-06-053-4/+31
| | | | https://github.com/veg/hyphy/releases/tag/2.5.31
* biology/jalview: Broken on 11Yuri Victorovich2021-06-052-4/+3
| | | | | | Also fix number of lines in pkg-descr, and replace space with tab. Reported by: fallout
* biology/seqan3: Update 3.0.2-1195 -> 3.0.3Yuri Victorovich2021-05-303-7/+16
| | | | Reported by: portscout
* biology/minimap2: Update to 2.20Jason W. Bacon2021-05-293-14/+30
| | | | | | Add "extra" binaries to install Changes: https://github.com/lh3/minimap2/releases/tag/v2.20
* biology/taxonkit: New port: Practical and efficient NCBI taxonomy toolkitYuri Victorovich2021-05-264-0/+35
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* biology/unikmer: New port: Toolkit for nucleic acid k-mer analysis, set ↵Yuri Victorovich2021-05-264-0/+37
| | | | operations on k-mers
* biology/bowtie2: Update to 2.4.4Jason W. Bacon2021-05-242-4/+4
| | | | | | Fix deadlock issue in multithreaded execution Reported by: portscout
* biology/py-resdk: Update 13.2.0 -> 13.3.0Yuri Victorovich2021-05-242-4/+4
| | | | Reported by: portscout
* biology/seqkit: Update 0.16.0 -> 0.16.1Yuri Victorovich2021-05-202-6/+6
| | | | Reported by: portscout
* biology/iolib: Drop maintainershipDanilo Egea Gondolfo2021-05-191-1/+1
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* - Update Unipro UGENE to version 38.1 and thus unbreakAlexey Dokuchaev2021-05-182-8/+6
| | | | - CONFIG defaults to 64-bit mode now, adjust the check
* biology/bowtie2: Update to 2.4.3Jason W. Bacon2021-05-173-43/+26
| | | | | | | | Drop tbb dependency (upstream switched to C++ threads) Add support for powerpc64 Reported by: portscout Tested by: pkubaj (powerpc64*)
* biology/ucsc-userapps: Update to v414Jason W. Bacon2021-05-153-11/+13
| | | | | Update license message. Confirmed via conversation with UCSC that some proprietary code is used in the "free" tools build. UCSC is working on it.
* *: Remove unnecessary 'port' argument from USES=readlineYasuhiro Kimura2021-05-151-1/+1
| | | | | PR: 248459 Exp-run by: antoine
* biology/cytoscape: mark unconditionally BROKENDmitry Marakasov2021-05-121-3/+1
| | | | Approved by: portmgr blanket
* biology/ugene: mark BROKEN (does not fetch)Dmitry Marakasov2021-05-121-0/+1
| | | | Approved by: portmgr blanket
* biology/seqan3: Correct dependenciesYuri Victorovich2021-05-121-3/+3
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* biology/seqan3: Add dependency math/lemonYuri Victorovich2021-05-121-0/+2
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* New port: biology/seqan3: C++ header-only library for biological sequence ↵Yuri Victorovich2021-05-125-0/+716
| | | | analysis
* biology/libsbml: Rename LIBXML option to LIBXML2Po-Chuan Hsieh2021-05-111-6/+5
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* math/py-matplotlib: chase minimum Python version in dependent portsThierry Thomas2021-05-103-3/+3
| | | | | | | | | Since the previous update changed USES=python from 3.6+ to 3.7+, all dependent ports must have USES=python:3.7+ as well, otherwise it breaks the @py36 flavor. PR: 255347 Reported by: sunpoet
* biology/mothur: Update 1.45.2 -> 1.45.3Yuri Victorovich2021-05-092-4/+4
| | | | Reported by: portscout
* Deorbit RESTRICTED && NO_CDROM, part two.Mathieu Arnold2021-05-063-3/+18
| | | | | | | | | Move ports to the licenses framework. RESTRICTED → auto-accept (unless expressly stated otherwise) NO_CDROM → dist-mirror pkg-mirror auto-accept Differential Revision: https://reviews.freebsd.org/D30010
* Deorbit RESTRICTED && NO_CDROM, part one.Mathieu Arnold2021-05-064-9/+4
| | | | | | | | For ports that already use the licenses framwork, merge the content of RESTRICTED/NO_CDROM/LEGAL* entries into LICENSEs. Approved by: rene Differential Revision: https://reviews.freebsd.org/D30010
* biology/py-resdk: Update 13.1.0 -> 13.2.0Yuri Victorovich2021-05-052-4/+6
| | | | Reported by: portscout
* biology/py-cutadapt: Update strict py-dnaio dep versionJason W. Bacon2021-05-041-1/+2
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* biology/py-dnaio: Update to 0.5.1Jason W. Bacon2021-05-043-7/+7
| | | | Add py.typed and distribute .pyi files
* Clean up some thingsTobias Kortkamp2021-05-011-2/+0
| | | | | | | | | | - Fix typos - Remove duplicate variables - Remove nop variables - Clean up commented PORTREVISION - Add missing USES Reported by: portscan
* biology/py-orange3-bioinformatics: Update 3.2.2 -> 4.3.1Yuri Victorovich2021-04-272-7/+12
| | | | Reported by: portscout
* biology/ncbi-entrez-direct: Update to 14.9.20210423_1Jason W. Bacon2021-04-265-41/+17
| | | | A few fixes to pass upstream test script
* devel/libepoll-shim: update to 0.0.20210418Jan Beich2021-04-262-11/+1
| | | | | | | Changes: https://github.com/jiixyj/epoll-shim/compare/v0.0.20210322...v0.0.20210418 Reported by: portscout Approved by: manu Differential Revision: https://reviews.freebsd.org/D29822
* biology/jalview: Update 2.07 -> 2.11.1.4Yuri Victorovich2021-04-256-80/+62
| | | | Take maintainership.
* Hook biology/ucsc-userapps to the buildAntoine Brodin2021-04-251-0/+1
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* biology/ucsc-userapps: Command line tools from the UCSC Genome Browser projectJason W. Bacon2021-04-2513-0/+342
| | | | | | | | | These are the command-line bioinformatics utilities associated with the UCSC genome browser. Care has been taken to install only the freely available tools. However, the license information at https://genome.ucsc.edu/license/ is not entirely clear and we may add non-free utilities in the future. Contact UCSC if you are using this port for commercial purposes.
* biology/ncbi-entrez-direct: Access to the NCBI's interconnected databasesJason W. Bacon2021-04-2411-0/+268
| | | | | | Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.
* biology/viennarna: Update 2.4.17 -> 2.4.18Yuri Victorovich2021-04-243-4/+5
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* biology/py-pyfaid: Update 0.5.9.2 -> 0.5.9.5Yuri Victorovich2021-04-232-4/+4
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* biology/abyss: Update 2.3.0-3 -> 2.3.1Yuri Victorovich2021-04-222-5/+4
| | | | Reported by: portscout
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