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* Update Qt5 to 5.12.0tcberner2018-12-161-0/+11
* New port: biology/py-fastTSNE: Fast, parallel implementations of t-SNEyuri2018-12-155-0/+47
* Bump PORTREVISION for ports depending on the canonical version of GCCgerald2018-12-1237-20/+37
* devel/boost-*: update to 1.69.0jbeich2018-12-125-3/+5
* Remove biology/njplotjrm2018-12-115-111/+0
* biology/mummer: Add USES=compiler:c++11-langyuri2018-12-111-1/+1
* biology/mummer: Update 3.23 -> 4.0.0beta2-2yuri2018-12-113-47/+61
* biology/mummer: Take maintainershipyuri2018-12-111-1/+1
* New port: math/checkm: Quality assessment tool for the microbial genomesyuri2018-12-074-0/+43
* New port: math/groopm: Metagenomic binning suiteyuri2018-12-074-0/+35
* devel/gradle: Update to 5.0yuri2018-12-052-4/+4
* biology/gatk: Change gradle4->gradle because it builds fine with both gradle ...yuri2018-12-041-2/+2
* biology/gatk: Correct the targetyuri2018-12-031-1/+1
* New port: biology/gatk: Variant discovery in high-throughput sequencing datayuri2018-12-036-0/+118
* Mark QT4 ports/functionality for removal on 2019-03-15rene2018-12-021-0/+3
* biology/igv: Update 2.4.15 -> 2.4.16yuri2018-11-192-6/+6
* biology/molden: update to 5.8.2jmd2018-11-133-10/+45
* biology/seqan-apps: fix build with GCC-based architecturesswills2018-11-101-2/+4
* biology/molden: Unbreak: fix the problem that it can't find libgcc_s.so from gccyuri2018-11-071-1/+2
* Fix build failure with base GCC because of double typedefs.linimon2018-11-061-0/+48
* Remove the incorrect typedefs to fix build on tier-2.linimon2018-11-062-0/+29
* Remove the inccorrect typedefs to fix build on tier-2.linimon2018-11-061-4/+0
* biology/igv: Update 2.4.10 -> 2.4.15yuri2018-11-053-24/+21
* biology/canu: Upgrade to 1.8, add experimental SLURM integrationjwb2018-11-045-31/+102
* biology/bowtie: Patch for gcc8 and clean upjwb2018-11-042-6/+17
* biology/bowtie: Revert previous commit with missing log messagejwb2018-11-042-17/+5
* biology/bowtie: Patchjwb2018-11-042-5/+17
* biology/py-loompy: Update 2.0.15 -> 2.0.16yuri2018-10-302-4/+4
* biology/iqtree: Update to version 1.6.8jrm2018-10-292-4/+4
* Fix build with tier-2 arches.linimon2018-10-281-1/+7
* biology/py-pyfaidx: Update 0.5.5.1 -> 0.5.5.2yuri2018-10-282-4/+4
* biology/p5-transdecoder: Upgrade to 5.4.0jwb2018-10-234-30/+44
* biology/hyphy: Update to version 2.3.14.16jrm2018-10-203-5/+11
* biology/py-loompy: Update 2.0.14 -> 2.0.15yuri2018-10-192-4/+4
* New port: biology/py-gffutils: Work with GFF and GTF files in a flexible data...yuri2018-10-194-0/+36
* New port: biology/py-pyfaidx: Efficient pythonic random access to fasta subse...yuri2018-10-194-0/+38
* New port: biology/py-gtfparse: Parsing tools for GTF (gene transfer format) f...yuri2018-10-194-0/+32
* biology/ngs-sdk: Update 2.9.2 -> 2.9.3yuri2018-10-193-5/+5
* biology/py-orange3-single-cell: Update 0.8.1 -> 0.8.2yuri2018-10-172-4/+4
* biology/iqtree: Update to version 1.6.7.1jrm2018-10-162-4/+4
* biology/py-orange3-single-cell: Update 0.8.0 -> 0.8.1yuri2018-10-142-6/+11
* biology/py-orange3-bioinformatics: Update 3.2.0 -> 3.2.2yuri2018-10-142-4/+4
* Deprecate most glib12 consumersantoine2018-10-121-0/+3
* Update devel/tbb to version 2019.1 and bump dependent ports' revisionsmartymac2018-10-111-1/+1
* Update to 1.73sunpoet2018-10-102-6/+10
* New port: biology/ncbi-cxx-toolkit: NCBI C++ Toolkityuri2018-10-085-0/+70
* biology/ncbi-toolkit: Update 2012.06.20 -> 2017.01.06yuri2018-10-086-175/+87
* biology/tinker: Update 7.1.3 -> 8.4.4; Move to science/yuri2018-10-0713-1004/+0
* biology/py-biom-format: Update to version 2.1.7jrm2018-10-062-16/+14
* Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, exceptdes2018-10-0615-30/+30
* Update devel/tbb to version 2019 and bump dependent port's revisionsmartymac2018-10-041-0/+1
* - Update to 1-14-10danilo2018-09-294-8/+9
* - Unbreak by adding missing pkg-plistwen2018-09-282-2/+136
* Allow building on powerpc64.linimon2018-09-281-1/+1
* Update Objective-C LLVM version to 6.0.brooks2018-09-261-1/+1
* Change 4 ports from net/mpich2 to net/mpichyuri2018-09-231-3/+5
* - Update to 1.63wen2018-09-222-4/+4
* Fix build on gcc-based archs by updating USES.linimon2018-09-221-1/+1
* Update to 1.5.2sunpoet2018-09-222-6/+7
* New port: biology/py-loompy: Work with .loom files for single-cell RNA-seq datayuri2018-09-214-0/+44
* biology/py-cutadapt: Upgrade to 1.18jwb2018-09-203-50/+9
* biology/ngs-sdk: Update 2.9.1 -> 2.9.2yuri2018-09-203-5/+5
* Upgrade these ports to USES=compiler:c++11-lang to fix build on gcc-basedlinimon2018-09-181-1/+1
* More precisely specify USES=compiler to fix build on gcc-basedlinimon2018-09-183-3/+3
* biology/py-pysam: Update 0.15.0 -> 0.15.1yuri2018-09-182-4/+4
* Add DOCS options to ports that should have one.mat2018-09-103-0/+6
* biology/seaview: Fix build with Clang 6tobik2018-09-083-0/+65
* Update science/hdf5 to 1.10.2sunpoet2018-09-061-1/+1
* Update to 1.31.0jhale2018-09-0317-181/+201
* biology/stacks: Enable OpenMP (oversight in previous commit)jwb2018-09-011-2/+2
* biology/iqtree: Update to version 1.6.7jrm2018-08-272-5/+4
* biology/py-bx-python: Update 0.8.1 -> 0.8.2yuri2018-08-262-5/+5
* biology/unanimity: Upgrade to latest release, soften dep version requirementsjwb2018-08-262-11/+10
* biology/protomol: Fix doubled USES overwriting the old valuetobik2018-08-251-3/+2
* biology/protomol: Fix build with Clang 6tobik2018-08-251-0/+1
* biology/primer3: Fix build with Clang 6tobik2018-08-251-0/+24
* biology/libsbml: Fix build with Clang 6tobik2018-08-251-9/+2
* biology/avida: Fix build with Clang 6tobik2018-08-251-0/+1
* biology/lamarc: Fix build with Clang 6tobik2018-08-251-0/+2
* Mark as broken with clang6 after r473289.linimon2018-08-241-1/+9
* - Update to 1.72wen2018-08-242-5/+4
* Remove expired ports:rene2018-08-176-104/+0
* biology/cytoscape: Fix licenseyuri2018-08-122-3/+5
* Mark as broken on arm.linimon2018-08-121-0/+4
* devel/boost-*: update to 1.68.0jbeich2018-08-095-2/+5
* biology/py-orange3-bioinformatics: Update 3.1.1 -> 3.2.0yuri2018-08-092-4/+4
* biology/py-orange3-single-cell: Update 0.7.0 -> 0.8.0yuri2018-08-092-4/+4
* Regular sorting of categories Makefiles.mat2018-08-081-1/+1
* New port: biology/py-orange3-single-cell: Orange add-on for gene expression o...yuri2018-08-074-0/+43
* biology/vcftools: Update to 0.1.16, a security releasejwb2018-08-042-4/+4
* biology/bcftools: update to 1.9fernape2018-08-035-24/+41
* biology/samtools: update to 1.9fernape2018-08-032-8/+7
* biology/htslib: update to 1.9fernape2018-08-032-6/+8
* biology/py-pysam: Update 0.14.1 -> 0.15.0yuri2018-07-313-8/+5
* Bump PORTREVISION for ports depending on the canonical version of GCCgerald2018-07-3015-10/+15
* biology/linux-foldingathome: reset maintainer by requesteadler2018-07-271-1/+1
* biology/seaview: Updatye version 4.6.5=>4.7bofh2018-07-222-4/+4
* biology/molden: Unbreak by updating the MASTER_SITES URLyuri2018-07-201-2/+1
* Mark BROKEN: unfetchaableantoine2018-07-201-0/+1
* biology/htslib: Update 1.6 -> 1.8yuri2018-07-174-10/+8
* Deprecate unmaintained ports under the NONE licenseantoine2018-07-131-0/+3
* biology/molden: Unbreak by updating the MASTER_SITES URLyuri2018-07-131-2/+1
* Mark BROKEN: unfetchableantoine2018-07-131-0/+1
* New port: biology/exonerate: Generic tool for sequence alignmentyuri2018-07-135-0/+67
* biology/py-orange3-bioinformatics: Update 3.1.0 -> 3.1.1yuri2018-07-132-4/+4
* New port: biology/stringtie: Transcript assembly and quantification for RNA-seqyuri2018-07-128-0/+157
* biology/hmmer: update to 3.2.1swills2018-07-114-46/+23
* biology/iqtree: Update to version 1.6.6jrm2018-07-092-4/+4
* New port: biology/cytoscape: Software to visualize molecular interaction netw...yuri2018-07-034-0/+83
* Mark various ports broken on mips64 and, where appropriate, mips.linimon2018-07-021-2/+4
* Mark BROKEN: missing plistantoine2018-06-291-0/+3
* Replace bsd.qt.mk by Uses/qt.mk and Uses/qt-dist.mktcberner2018-06-292-4/+4
* New port: biology/igv: Visualization tool for genomic datasetsyuri2018-06-266-0/+77
* Mark as broken on aarch64.linimon2018-06-251-0/+2
* - Update to 5.17.0wen2018-06-253-4/+5
* biology/phyml: update to v3.3.20180621fernape2018-06-232-5/+6
* Update math/gsl to 2.5tcberner2018-06-231-0/+1
* biology/ngs-sdk: Update 2.9.0 -> 2.9.1yuri2018-06-223-5/+5
* Mark these ports as broken on aarch64.linimon2018-06-222-0/+4
* Mark as broken on aarch64, and, where appropriate, armvX.linimon2018-06-224-0/+16
* Use PY_FLAVOR for dependencies.mat2018-06-216-13/+13
* Mark as broken on powerpc64 pending fix for PR 199603.linimon2018-06-191-0/+2
* Adjust USES to fix builds on gcc-based architectures.linimon2018-06-191-1/+1
* Mark ports broken on powerpc64, categories a-c.linimon2018-06-181-3/+4
* biology/bedtools: Fix Makefile to respect PREFIXjwb2018-06-172-0/+22
* New port: biology/py-orange3-bioinformatics: Orange add-on providing common f...yuri2018-06-144-0/+41
* biology/py-Genesis-PyAPI: Remove stray USES=fortranyuri2018-06-131-1/+1
* New port: biology/py-Genesis-PyAPI: API for the Genesis platform for genetics...yuri2018-06-134-0/+29
* biology/artemis: Update 9 -> 17.0.1-11yuri2018-06-124-1719/+72
* New port: biology/ngs-sdk: Tools and libraries for using data in the INSDC Se...yuri2018-06-119-0/+256
* Remove expired ports:rene2018-06-0751-1777/+0
* Update to 2.0.0 and pass maintainership to committer.krion2018-06-068-345/+121
* Add new port: biology/infernalkrion2018-06-066-0/+117
* Mark as broken on powerpc64. The entire, unhelpful, error message is:linimon2018-06-031-0/+2
* Adjust USES to fix building on gcc-based archs (in particular, powerpc64).linimon2018-06-031-1/+1
* Update WWWsunpoet2018-05-2813-13/+13
* biology/hyphy: Update to version 2.3.13jrm2018-05-233-5/+10
* biology/clustal-omega: Multiple alignment of nucleic acid and protein, replac...jwb2018-05-225-0/+64
* biology/clustalx: Multiple alignment of nucleic acid and protein sequences wi...jwb2018-05-225-0/+59
* biology/clustalw: Fix license, take maintainershipjwb2018-05-212-5/+6
* biolog/molden: unbreak after at least two intransparent distfile updatesjmd2018-05-212-6/+4
* biology/fastx-toolkit: Fix build on FreeBSD 12jwb2018-05-162-2/+19
* Add upstream patch to fix the build with Qt 5.10.rakuco2018-05-162-1/+31
* - Update to 3.3.20180214wen2018-05-152-5/+6
* biology/diamond: Update to version 0.9.22jrm2018-05-152-4/+4
* biology/hyphy: Bump PORTREVISION after upstream rerolled releasejrm2018-05-153-14/+4
* biology/py-biopython: Unbreak on python3; Add licenseyuri2018-05-141-2/+9
* biology/iqtree: Update to version 1.6.5jrm2018-05-122-4/+4
* New port, biology/hyphy: Hypothesis testing using Phylogeniesjrm2018-05-117-0/+645
* Mark BROKEN: checksum and size mismatchantoine2018-05-071-0/+2
* Deprecate ports broken for more than 6 monthsantoine2018-05-055-0/+10
* biology/iqtree: Update to version 1.6.4jrm2018-05-012-4/+4
* biology/paml: Set PORTVERSION directlyjrm2018-04-261-1/+1
* biology/canu: Upgrade to 1.7 releasejwb2018-04-265-37/+51
* biology/paml: Update to version 4.9hjrm2018-04-263-27/+181
* Switch all pypi.python.org WWWs to a new PyPi home pypi.org whereamdmi32018-04-262-2/+2
* biology/unanimity: Pacific Biosciences consensus library and applicationsjwb2018-04-2411-0/+146
* biology/seaview: Update version 4.6.3=>4.6.5bofh2018-04-242-6/+8
* biology/pbcopper: Core C++ library for Pacific Biosciences toolsjwb2018-04-246-0/+133
* biology/pbbam: PacBio BAM C++ library, with SWIG bindingsjwb2018-04-245-0/+182
* biology/pbseqan: Pacific Biosciences patched and stripped down SeqAnjwb2018-04-225-0/+698
* biology/diamond: Update to version 0.9.21jrm2018-04-212-5/+4
* biology/ddocent: Bash pipeline for RAD sequencingjwb2018-04-208-0/+617
* biology/freebayes: Bayesian haplotype-based polymorphism discovery and genoty...jwb2018-04-2014-0/+293
* biology/bedtools: Upgrade to 2.27.1jwb2018-04-206-54/+36
* devel/boost-*: update to 1.67.0jbeich2018-04-182-1/+2
* biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF filesjwb2018-04-178-0/+511
* biology/fastahack: Utility for indexing and sequence extraction from FASTA filesjwb2018-04-166-0/+99
* biology/smithwaterman: Smith-waterman-gotoh alignment algorithmjwb2018-04-166-0/+149
* biology/tabixpp: C++ wrapper to tabix indexerjwb2018-04-155-0/+131
* - Update to 1.71wen2018-04-092-5/+4
* biology/pear-merger: Memory-efficient and accurate paired-end read mergerjwb2018-04-054-0/+37
* biology/seqtk: Tool for processing sequences in FASTA/FASTQ formatjwb2018-04-045-0/+51
* biology/trimadap: Trim adapter sequences from Illumina datajwb2018-04-046-0/+65
* biology/rainbow: Efficient clustering and assembling of short readsjwb2018-04-035-0/+50
* - Update to 1.61wen2018-04-012-6/+7
* biology/stacks: Software pipeline for building loci from short-read sequencesjwb2018-03-317-0/+136
* biology/libgtextutils: Unbreak for FreeBSD 12jwb2018-03-292-1/+12
* biology/bamtools: API and toolkit for handling BAM filesjwb2018-03-287-0/+76
* biology/ncbi-blast+: Upgrade to 2.7.1jwb2018-03-286-377/+409
* biology/iqtree: Update to version 1.6.3jrm2018-03-232-5/+4
* biology/py-pysam: Update to 0.14.1yuri2018-03-212-5/+5
* Mark broken on armvX and mips.linimon2018-03-181-0/+4
* Mark the latest version broken on armvX. Note: 2.1.8.3 built ok.linimon2018-03-181-0/+3
* biology/diamond: Update to version 0.9.19jrm2018-03-172-5/+4
* biology/diamond: Update to version 0.9.18-49jrm2018-03-152-4/+5
* Return maho@'s ports to the pool after his commit bit expired.rene2018-03-111-1/+1
* Remove now-useless, commented-out lines.linimon2018-03-111-4/+0
* Bump PORTREVISIONs of all users of math/mpc that we just updated togerald2018-03-1121-15/+21
* biology/seqan-apps, biology/seqan: Update to 2.4.0yuri2018-03-107-1269/+90
* biology/iqtree: Update to version 1.6.2jrm2018-03-032-5/+4
* Reduce dependency on the python2 metaportantoine2018-02-191-1/+2
* biology/py-pysam: Update to 0.14yuri2018-02-112-4/+4
* biology/py-bx-python: Update to 0.8.1yuri2018-02-102-8/+9
* Canonicalize PyPi WWWs:amdmi32018-02-091-1/+1
* biology/diamond: Update to version 0.9.17jrm2018-02-022-4/+4
* - Update to 3.3.20180129wen2018-02-012-5/+4
* Multiple ports:jwb2018-01-3116-29/+16
* devel/boost-*: update to 1.66.0jbeich2018-01-182-1/+2
* - Convert to option helper install target (add OPTIONS_DEFINE=DOCSdanfe2018-01-121-2/+4
* Update Qt5 ports to 5.9.3.rakuco2018-01-071-0/+10
* biology/seaview: Update version 4.6.2=>4.6.3bofh2018-01-063-7/+8
* New USES=eigentcberner2018-01-031-5/+2
* - Update to 3.697wen2018-01-012-3/+4
* - Update to 5.16.0wen2018-01-013-4/+9
* biology/iqtree: Fix distinfo after upstream re-released v1.6.1jrm2017-12-302-3/+4
* biology/iqtree: Update to version 1.6.1jrm2017-12-292-9/+8
* Disable the extra flag "-march=native" on arm to fix builds.linimon2017-12-271-3/+6
* Update to 2.0.1sunpoet2017-12-273-5/+31
* biology/canu: Replace += with = for dependsjwb2017-12-221-2/+2
* - Fix build on 11+amdmi32017-12-222-4/+11
* [new port] biology/canu: Single molecule sequence assemblerjwb2017-12-226-0/+167
* Try to bring some consistency to ports that have x86-specific pieces.linimon2017-12-212-12/+12
* Switch from swig 2.0 to swig 3.0bapt2017-12-211-2/+4
* Mark more recently failing ports broken on aarch64.linimon2017-12-191-2/+3
* Back out previous commits by jbeich demand.linimon2017-12-182-10/+2
* Bah. Remove spare line from cut-and-paste.linimon2017-12-181-1/+0
* Attempt to fix build on non-x86 archs. Untested, but does no harmlinimon2017-12-182-2/+11
* biology/diamond: Update to version 0.9.14jrm2017-12-142-4/+4
* biology/seqtools: re-try on powerpc* after r449590jbeich2017-12-121-2/+0
* - Those ports fail to build with python3antoine2017-12-121-1/+1
* Mark several ports newly broken on arm.linimon2017-12-112-3/+9
* biology/py-biom-format: Add required dependency on math/py-pandas and dojrm2017-12-101-3/+7
* [new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for adap...jwb2017-12-095-0/+47
* These are also broken on aarch64 in the same way as armv6/7.linimon2017-12-091-0/+1
* Mark more ports broken that fail on both armv6 and armv7.linimon2017-12-091-0/+3
* Revert previous fat-fingered commit. These are the error messages fromlinimon2017-12-081-2/+2
* Update errror message on armvX.linimon2017-12-081-2/+2
* biology/fasttree: update to version 2.1.10jwb2017-12-054-19/+45
* biology/py-macs2: Restrict to python 2.7.jwb2017-12-051-2/+2
* Add a USES=python:env, that will not add a dependency on Python.mat2017-12-042-4/+2
* Fix configure options for gnustep-maketheraven2017-12-031-1/+1
* [new port] biology/py-macs2: Analysis of chromatin immunoprecipitation (ChIP)...jwb2017-12-034-0/+41
* [new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq ...jwb2017-12-035-0/+91
* Fix packaging with python3antoine2017-12-012-14/+14
* [unbreak] biology/bwa: Remove old patch filesjwb2017-12-013-37/+0
* [new port] biology/fastqc: Quality control tool for high throughput sequence ...jwb2017-12-015-0/+260
* biology/py-cutadapt: Remove MASTER_SITE_SUBDIR per mentor commentjwb2017-12-011-1/+0
* Convert Python ports to FLAVORS.mat2017-11-309-17/+15
* For ports that are marked BROKEN on armv6, and also fail to build onlinimon2017-11-305-0/+5
* biology/bowtie2: Upgrade to 2.3.3.1jwb2017-11-305-50/+19
* [new port] biology/py-cutadapt: Finds and removes adapter sequences, primers, pojwb2017-11-305-0/+74
* biology/bwa: Upgrade to 0.7.17jwb2017-11-282-5/+10
* biology/vcftools: Upgrade to latest release 0.1.15jwb2017-11-282-4/+4
* - Switch to options helpersamdmi32017-11-261-1/+5
* biology/diamond: Update to version 0.9.13jrm2017-11-182-4/+4
* - Update to 3.1b2wen2017-11-115-39/+69
* Fix the context of some patches so that they apply with stricter patch(1)antoine2017-11-102-6/+6
* biology/diamond: Update to version 0.9.12jrm2017-11-092-7/+5
* Fix USE_GITHUB usage.mat2017-11-062-5/+4
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