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ate-1.16&id=bf18938c8bc82d7632d2b1c08f99d164cae870fd'>Reset inactive maintainer who has not responded to email. or nucleic acid k-mer analysis, set opera...
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* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-1/+0
* Set license information and NO_ARCHMateusz Piotrowski2020-11-121-0/+5
linimon2006-09-041-1/+1
Yuri Victorovich2021-05-274-0/+37
* biology/bowtie2: Update to 2.4.4Jason W. Bacon2021-05-252-4/+4
* biology/py-resdk: Update 13.2.0 -> 13.3.0Yuri Victorovich2021-05-242-4/+4
* biology/seqkit: Update 0.16.0 -> 0.16.1Yuri Victorovich2021-05-202-6/+6
* biology/iolib: Drop maintainershipDanilo Egea Gondolfo2021-05-201-1/+1
* - Update Unipro UGENE to version 38.1 and thus unbreakAlexey Dokuchaev2021-05-182-8/+6
* biology/bowtie2: Update to 2.4.3Jason W. Bacon2021-05-183-43/+26
* biology/ucsc-userapps: Update to v414Jason W. Bacon2021-05-153-11/+13
* *: Remove unnecessary 'port' argument from USES=readlineYasuhiro Kimura2021-05-151-1/+1
* biology/cytoscape: mark unconditionally BROKENDmitry Marakasov2021-05-121-3/+1
* biology/ugene: mark BROKEN (does not fetch)Dmitry Marakasov2021-05-121-0/+1
* biology/seqan3: Correct dependenciesYuri Victorovich2021-05-121-3/+3
* biology/seqan3: Add dependency math/lemonYuri Victorovich2021-05-121-0/+2
* New port: biology/seqan3: C++ header-only library for biological sequence ana...Yuri Victorovich2021-05-125-0/+716
* biology/libsbml: Rename LIBXML option to LIBXML2Po-Chuan Hsieh2021-05-121-6/+5
* math/py-matplotlib: chase minimum Python version in dependent portsThierry Thomas2021-05-113-3/+3
* biology/mothur: Update 1.45.2 -> 1.45.3Yuri Victorovich2021-05-102-4/+4
* Deorbit RESTRICTED && NO_CDROM, part two.Mathieu Arnold2021-05-063-3/+18
* Deorbit RESTRICTED && NO_CDROM, part one.Mathieu Arnold2021-05-064-9/+4
* biology/py-resdk: Update 13.1.0 -> 13.2.0Yuri Victorovich2021-05-062-4/+6
* biology/py-cutadapt: Update strict py-dnaio dep versionJason W. Bacon2021-05-041-1/+2
* biology/py-dnaio: Update to 0.5.1Jason W. Bacon2021-05-043-7/+7
* Clean up some thingsTobias Kortkamp2021-05-021-2/+0
* biology/py-orange3-bioinformatics: Update 3.2.2 -> 4.3.1Yuri Victorovich2021-04-272-7/+12
* biology/ncbi-entrez-direct: Update to 14.9.20210423_1Jason W. Bacon2021-04-275-41/+17
* devel/libepoll-shim: update to 0.0.20210418Jan Beich2021-04-262-11/+1
* biology/jalview: Update 2.07 -> 2.11.1.4Yuri Victorovich2021-04-266-80/+62
* Hook biology/ucsc-userapps to the buildAntoine Brodin2021-04-261-0/+1
* biology/ucsc-userapps: Command line tools from the UCSC Genome Browser projectJason W. Bacon2021-04-2613-0/+342
* biology/ncbi-entrez-direct: Access to the NCBI's interconnected databasesJason W. Bacon2021-04-2511-0/+268
* biology/viennarna: Update 2.4.17 -> 2.4.18Yuri Victorovich2021-04-243-4/+5
* biology/py-pyfaid: Update 0.5.9.2 -> 0.5.9.5Yuri Victorovich2021-04-242-4/+4
* biology/abyss: Update 2.3.0-3 -> 2.3.1Yuri Victorovich2021-04-232-5/+4
* biology/py-crossmap: Update to 0.5.4Jason W. Bacon2021-04-212-5/+4
* biology/py-crossmap: Fix build with Python 3.8+Kai Knoblich2021-04-211-1/+5
* biology/py-bigwig: Fix packaging with Python 3.8+Kai Knoblich2021-04-211-1/+1
* New port: biology/py-resdk: Resolwe SDK to interact with Resolwe server and R...Yuri Victorovich2021-04-204-0/+38
* biology/snpeff: Improvements to Makefile and patchesJason W. Bacon2021-04-204-12/+13
* biology/abyss: Update 2.2.5 -> 2.3.0-3Yuri Victorovich2021-04-193-6/+11
* biology/snpeff: Genetic variant annotation and effect prediction toolboxJason W. Bacon2021-04-197-0/+180
* biology/bbmap: BBMap short read aligner, and other bioinformatic toolsJason W. Bacon2021-04-196-0/+2064
* biology/bowtie2: Add support for powerpc64leJason W. Bacon2021-04-183-4/+17
* biology/readseq: Remove $FreeBSD$ tag inserted to silence portlintJason W. Bacon2021-04-181-2/+0
* biology/readseq: Read and reformat biosequences, Java command-line versionJason W. Bacon2021-04-185-0/+38
* biology/seqkit: Change WWW to the project URL (from GitHub URL)Yuri Victorovich2021-04-171-1/+1
* New port: biology/seqkit: Cross-platform and ultrafast toolkit for FASTA/Q fi...Yuri Victorovich2021-04-174-0/+42
* biology/ngs-sdk: Fix build on non-amd64 architectures that was broken by expl...Yuri Victorovich2021-04-161-1/+1
* Clean up some thingsTobias Kortkamp2021-04-151-1/+0
* devel/onetbb: Update to 2021.2.0 and bump dependenciesGanael LAPLANCHE2021-04-141-1/+1
* biology/diamond: Update to 2.0.9Joseph Mingrone2021-04-132-4/+4
* biology/mothur: Update to 1.45.2Jason W. Bacon2021-04-134-28/+25
* biology/py-crossmap: Lift over genomics coordinates between assembliesJason W. Bacon2021-04-136-0/+59
* biology/py-bigwig: Python access to bigWig files using libBigWigJason W. Bacon2021-04-134-0/+30
* biology/ncbi-vdb: Restore static libs installed with symlinks as shared libs ...Yuri Victorovich2021-04-132-3/+18
* biology/ngs-sdk: Restore static libs installed with symlinks as shared libs a...Yuri Victorovich2021-04-132-3/+9
* New port: biology/ncbi-vdb: NCBI's virtualized back-end for accessing Sequenc...Yuri Victorovich2021-04-1231-0/+947
* biology/ngs-sdk: Improve the 'install' target and other parts of Makefile, re...Yuri Victorovich2021-04-127-102/+62
* biology/minimap2: Update to 2.18Jason W. Bacon2021-04-123-9/+7
* biology/vsearch: Update to 2.17.0Jason W. Bacon2021-04-102-4/+4
* biology/hyphy: Update to 2.5.30Joseph Mingrone2021-04-082-4/+4
* Remove expired ports:Rene Ladan2021-04-0817-380/+0
* One more small cleanup, forgotten yesterday.Mathieu Arnold2021-04-07104-104/+0
* all: Remove all other $FreeBSD keywords.Mathieu Arnold2021-04-063-7/+1
* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-06187-188/+0
* biology/pear-merger: enable on aarch64, armv6, armv7, riscv64Piotr Kubaj2021-04-061-5/+0
* biology/trimadap: fix build on powerpc64lePiotr Kubaj2021-04-061-1/+8
* biology/pear-merger: fix build on non-x86Piotr Kubaj2021-04-061-0/+6
* biology/subread: Update to 2.0.2Jason W. Bacon2021-03-304-19/+20
* biology/molden: Fix build with gfortran10Yuri Victorovich2021-03-301-1/+9
* biology/igv: Update 2.8.13 -> 2.9.4Yuri Victorovich2021-03-293-42/+44
* biology/vcflib: fix build on powerpc64lePiotr Kubaj2021-03-291-0/+7
* biology/vsearch: Update to 2.16.0Jason W. Bacon2021-03-252-4/+4
* Mark ports recursively depending on Python 2.7 for expiration on June 23.Rene Ladan2021-03-242-0/+6
* biology/vcf2hap: Generate .hap file from VCF for haplohseqJason W. Bacon2021-03-244-0/+35
* biology/ad2vcf: Add allelic depth info from a SAM stream to a VCF fileJason W. Bacon2021-03-234-0/+36
* - Update Unipro UGENE to version 38.0Alexey Dokuchaev2021-03-235-28/+8
* Fix spelling mistakes, typos, poor wording, hyphenation, jargonisms,Alexey Dokuchaev2021-03-221-1/+1
* biology/vcf-split: Split a multi-sample VCF into single-sample VCFsJason W. Bacon2021-03-214-0/+35
* biology/biolibc: Low-level high-performance bioinformatics libraryJason W. Bacon2021-03-215-0/+33
* biology/htslib: Update to 1.12Jason W. Bacon2021-03-2117-148/+32
* biology/generand: Update to 0.1.2Jason W. Bacon2021-03-202-4/+4
* biology/py-multiqc: Update to 1.10Jason W. Bacon2021-03-202-4/+5
* biology/ngs-sdk: Update 2.10.9 -> 2.11.0Yuri Victorovich2021-03-203-5/+6
* PyQt5: Update PyQt5 to 5.15.4 and py-qtbuilder to 1.9.1Loïc Bartoletti2021-03-161-1/+1
* biology/generand: Generate random genomic data in FAST[AQ], SAM, or VCF formatJason W. Bacon2021-03-164-0/+27
* biology/abyss: Add PORTSCOUT lineYuri Victorovich2021-03-141-0/+2
* Move: biology/py-fastTSNE -> math/py-openTSNEYuri Victorovich2021-03-145-49/+0
* biology/gatk: Fix fetchYuri Victorovich2021-03-141-5/+5
* biology/gatk: Update 4.1.9.0 -> 4.2.0.0Yuri Victorovich2021-03-122-7/+6
* biology/diamond: Update to 2.0.8Joseph Mingrone2021-03-112-4/+4
* biology/hmmer: disable on powerpc64le and powerpcspePiotr Kubaj2021-03-111-1/+1
* biology/py-scikit-bio: fix build on powerpc64Piotr Kubaj2021-03-091-1/+1
* biology/py-scikit-bio: fix build on powerpc64lePiotr Kubaj2021-03-091-2/+5
* PyQt5: Update PyQt5 to 5.15.3, QScintilla2 to 2.12.0, py-qtbuilder to 1.9.0Loïc Bartoletti2021-03-081-1/+1
* Unbreak INDEXAntoine Brodin2021-03-071-1/+1
* py-cutadapt: Update to 3.3Jason W. Bacon2021-03-07