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* Fix after gets(3) retirement using gets_s(3).cy2019-09-021-1/+1
* Add a patch to remove use of gets(3)lwhsu2019-09-022-0/+169
* biology/py-pysam: Update 0.15.2 -> 0.15.3yuri2019-08-312-4/+4
* biology/ngs-sdk: Update 2.9.6 -> 2.10.0yuri2019-08-314-13/+13
* biology/iqtree: Update to version 1.6.12jrm2019-08-272-5/+4
* biology/gperiodic: fix NLS and other rough edgespi2019-08-232-30/+22
* devel/boost-*: update to 1.71.0jbeich2019-08-199-7/+9
* biology/checkm: Update 1.0.17 -> 1.0.18yuri2019-08-192-4/+4
* Convert to UCL & cleanup pkg-message (categories a-c)mat2019-08-1413-32/+78
* biology/bolt-lmm: Upgrade to 2.3.4jwb2019-08-137-120/+63
* biology/checkm: Update 1.0.16 -> 1.0.17yuri2019-08-122-4/+4
* biology/gperiodic: upgrade 2.0.10 -> 3.0.3pi2019-08-123-23/+39
* Update to 1.007005 (1.7.5)sunpoet2019-08-123-20/+5
* Update WWWsunpoet2019-08-111-1/+1
* biology/checkm: Update 1.0.13 -> 1.0.16yuri2019-08-092-5/+4
* biology/hhsuite: fix build on powerpc64pkubaj2019-08-051-2/+7
* PR: 239613jwb2019-08-056-1/+94
* biology/diamond: Update to version 0.9.25jrm2019-08-052-4/+4
* Mark BROKEN: unfetchableantoine2019-08-043-0/+6
* Bump PORTREVISION for ports depending on the canonical version of GCCgerald2019-07-2750-32/+50
* biology/gatk: Update 4.0.11.0 -> 4.1.2.0-43yuri2019-07-272-12/+31
* - Update WWWamdmi32019-07-251-1/+1
* Prepare for devel/gradle4 and java/openjfx8-devel updatestobik2019-07-231-2/+2
* biology/treekin: fix build on GCC architecturespkubaj2019-07-191-1/+2
* ncbi-blast+: Unbreak build with gcc8 following gcc9 patchjwb2019-07-132-7/+9
* New port: biology/libbigwig: C library for handling bigWig files (containing ...yuri2019-07-125-0/+54
* ncbi-blast+: Fix build with gcc9jwb2019-07-111-0/+14
* Update security/nettle to 3.5.1sunpoet2019-07-102-1/+2
* - Update WWWamdmi32019-07-081-1/+1
* biology/mothur: Update 1.42.2 -> 1.42.3yuri2019-06-282-4/+4
* Mark this port as not buildable on powerpc64:linimon2019-06-251-0/+2
* biology/iqtree: Update to version 1.6.11jrm2019-06-252-4/+4
* biology/viennarna: Make it less/not prone to failures due to hardcoded C++ li...yuri2019-06-255-29/+15
* New port: biology/viennarna: Alignment tools for the structural analysis of RNAyuri2019-06-249-0/+331
* Use USES=pathfixsunpoet2019-06-231-21/+14
* biology/abyss: fix build on big-endian architecturespkubaj2019-06-213-2/+20
* Enable workaround for building on powerpc64.linimon2019-06-211-2/+8
* biology/mothur: Update 1.42.1-3 -> 1.42.2yuri2019-06-202-6/+5
* biology/py-bx-python: Update 0.8.2 -> 0.8.4yuri2019-06-192-5/+4
* New port: biology/treekin: Efficient computation of RNA folding dynamicsyuri2019-06-164-0/+37
* biology/ncbi-blast+: Fix build on powerpc64, add run dep for update_blastdb.pljwb2019-06-141-4/+10
* biology/ncbi-blast+: Upgrade to 2.9.0jwb2019-06-133-6/+78
* biology/kallisto: Upgrade to 0.46.0jwb2019-06-122-4/+4
* biology/tRNAscan-SE: Update to 2.0.3swills2019-06-083-15/+8
* biology/igv: Update 2.5.2 -> 2.5.3yuri2019-06-022-6/+6
* biology/tRNAscan-SE: fix build with GCC-based architecturspkubaj2019-05-301-1/+3
* biology/cufflinks: Fix build on i386 by removing the hard-coded -m64yuri2019-05-291-0/+16
* biology/bolt-lmm: Mixed model association testing and variance component anal...jwb2019-05-269-0/+228
* New port: biology/cufflinks: Cufflinks assembles transcripts, estimates their...yuri2019-05-266-0/+80
* biology/hhsuite: Fix build on platforms where SIMD instruction set doesn't ex...yuri2019-05-222-0/+36
* biology/fastp: Remove redundant USE_GCCjwb2019-05-211-8/+1
* biology/mothur: Add USES=compiler:c++11-langyuri2019-05-211-1/+1
* New port: biology/mothur: Software for bioinformatics of the microbial ecolog...yuri2019-05-214-0/+41
* - Update to 3.3.20190321wen2019-05-202-5/+4
* - Update to 5.18.0wen2019-05-203-29/+22
* New port: biology/hhsuite: Remote protein homology detection suiteyuri2019-05-198-0/+128
* biology/gemma: Lowercase PORTNAME, remove unnecesary USE_GCCjwb2019-05-191-9/+3
* biology/gemma: Genome-wide Efficient Mixed Model Associationjwb2019-05-178-0/+431
* biology/jellyfish: Upgrade to 2.2.10, patch for powerpc64jwb2019-05-148-16/+79
* biology/vsearch: Update to 2.13.4jwb2019-05-114-91/+4
* biology/igv: Update 2.5.0 -> 2.5.2yuri2019-05-112-6/+6
* biology/trimadap: Mark only for amd64 and i386jwb2019-05-111-3/+2
* biology/stacks: Remove obsolete pkg-message regarding web interfacejwb2019-05-111-16/+0
* biology/stacks: Upgrade to 2.4jwb2019-05-113-52/+6
* biology/vsearch: Remove powerpc64 supportjwb2019-05-101-1/+1
* biology/vsearch: Versatile open-source tool for metagenomicsjwb2019-05-108-0/+163
* devel/openmp: phase outjbeich2019-05-092-1/+2
* biology/tRNAscan-SE: fix build with GCC-based architecturespkubaj2019-05-081-1/+1
* biology/minimap2: Upgrade to 2.17jwb2019-05-053-7/+9
* biology/ddocent: Upgrade to 2.7.8jwb2019-05-046-152/+86
* biology/fastp: Respect WITH_DEBUG - do not strip binaryjwb2019-05-041-1/+3
* These ports now build on aarch64.linimon2019-05-041-3/+1
* biology/fastp: Ultra-fast all-in-one FASTQ preprocessorjwb2019-05-035-0/+73
* biology/star: Force newer GCC on platforms with GCC 4.2 basejwb2019-05-021-1/+8
* biology/py-cutadapt: Upgrade to 2.3jwb2019-04-272-5/+4
* Clean up plistantoine2019-04-251-1/+1
* biology/minimap2: Pairwise aligner for genomic and spliced nucleotide sequencesjwb2019-04-255-0/+87
* biology/bowtie2: Clarify CPU-specificityjwb2019-04-251-1/+2
* biology/star: Modify PKGBASE to avoid conflict with archivers/starjwb2019-04-231-0/+1
* Fix typosunpoet2019-04-231-2/+2
* Sort PLISTsunpoet2019-04-232-23/+23
* Related to revision 499061 bump ports with USES=fortran to have themgerald2019-04-224-4/+4
* biology/star: Spliced Transcripts Alignment to a Referencejwb2019-04-226-0/+70
* biology/bowtie2: Upgrade to 2.3.5.1jwb2019-04-214-13/+42
* biology/canu: Fix build on powerpc64 and aarch64jwb2019-04-184-20/+141
* New port: biology/py-xenaPython: API for Xena Hub to access genetic informati...yuri2019-04-134-0/+32
* devel/boost-*: update to 1.70.0jbeich2019-04-127-3/+7
* Bump a few PORTREVISIONs after r498529antoine2019-04-105-1/+5
* Update devel/readline to 8.0sunpoet2019-04-091-1/+1
* Use real PORTVERSION of devel/p5-Parse-RecDescentsunpoet2019-04-061-1/+1
* biology/igv: Update 2.4.19 -> 2.5.0yuri2019-04-042-6/+6
* - Fix build in head i386danilo2019-04-021-0/+1
* biology/py-fastTSNE: Add the PORTSCOUT lineyuri2019-04-011-0/+2
* biology/ngs-sdk: Update 2.9.4 -> 2.9.6yuri2019-03-313-5/+5
* - Add LICENSEamdmi32019-03-301-4/+4
* Mark as broken on aarch64:linimon2019-03-301-0/+2
* biology/p5-TrimGalore: Upgrade to 0.6.1jwb2019-03-254-11/+39
* biology/py-cutadapt: Upgrade to 2.1jwb2019-03-252-7/+13
* Unbreakantoine2019-03-252-2/+2
* biology/py-dnaio: Read and write FASTQ and FASTAjwb2019-03-254-0/+27
* biology/bowtie2: Upgrade to 2.3.5jwb2019-03-195-41/+111
* Qt4 deprecation: Remove Qt4 and its consumes.tcberner2019-03-175-62/+0
* biology/cd-hit: Upgrade to 4.8.1jwb2019-03-154-14/+106
* biology/bedtools: unbreak with libc++ 8jbeich2019-03-041-0/+5
* biology/paml: Update to version 4.9ijrm2019-02-263-4/+6
* New port: biology/abyss: Assembly By Short Sequences: parallel, paired-end se...yuri2019-02-256-0/+116
* kallisto: Upgrade to 0.45.1, unbundle hstlibjwb2019-02-255-16/+65
* biology/unanimity: Upgrade to 3.4.1jwb2019-02-253-5/+5
* biology/ngs-sdk: Update 2.9.3 -> 2.9.4yuri2019-02-243-5/+5
* biology/igv: Update 2.4.16 -> 2.4.19yuri2019-02-242-6/+6
* biology/unanimity is not compatible with python 3.xantoine2019-02-232-2/+2
* Update to 1.007005 (1.7.5)sunpoet2019-02-233-17/+2
* biology/iqtree: Update to version 1.6.10jrm2019-02-212-5/+4
* Update to 1.007003sunpoet2019-02-214-67/+16
* Update to 1.007004 (1.7.4)sunpoet2019-02-215-998/+189
* Add p5-Bio-Cluster 1.7.3sunpoet2019-02-215-0/+55
* biology/pbseqan: Mark deprecatedjwb2019-02-201-0/+2
* biology/unanimity: Upgrade to 3.4.0jwb2019-02-2010-70/+133
* biology/pbbam: Upgrade to 0.18.0 releasejwb2019-02-204-23/+47
* biology/pbcopper: Upgrade to 0.4.1 releasejwb2019-02-205-38/+26
* vec_splats function is not supported by base GCC. Add USES=compiler:c11linimon2019-02-181-2/+2
* biology/pbseqan: Minor upgrade to latest commitjwb2019-02-182-6/+6
* Update dns/libidn2 to 2.1.1sunpoet2019-02-102-2/+2
* biology/checkm: Update 1.0.12 -> 1.0.13yuri2019-02-102-5/+4
* - Update WWWamdmi32019-02-071-1/+1
* biology/dsr-pdb: Correct typoyuri2019-02-061-1/+1
* biology/dsr-pdb: Add c++11 flags because boost isn't found without ityuri2019-02-063-2/+25
* New port: biology/figtree: Graphical viewer of phylogenetic treesyuri2019-02-044-0/+49
* New port: biology/graphlan: High-quality circular representations of taxonomi...yuri2019-02-045-0/+127
* New port: biology/prodigy-lig: Prediction of protein-small molecule binding a...yuri2019-02-044-0/+34
* New port: biology/prodigal: Protein-coding gene prediction for prokaryotic ge...yuri2019-02-044-0/+51
* Move Objective-C ports to the v2 GNUstep ABI.theraven2019-02-031-1/+1
* biology/py-loompy: Update 2.0.16 -> 2.0.17yuri2019-02-032-5/+5
* New port: biology/dsr-pdb: Simple C++ PDB reader (reads the protein descripti...yuri2019-01-299-0/+122
* biology/py-pysam: Update 0.15.1 -> 0.15.2yuri2019-01-262-4/+4
* Sort categories Makefiles.mat2019-01-231-1/+1
* Fix Qt5 symbol version scripts to put the catch-all clause first. Whentijl2019-01-163-2/+3
* biology/stacks: Upgrade to 2.3jwb2019-01-124-38/+14
* New port: biology/hisat2: Program for mapping next-generation sequencing readsjwb2019-01-127-0/+577
* Fixup bulk -a errors with BUILD_ALL_PYTHON_FLAVORS=yes.mat2019-01-111-1/+2
* biology/seqtools: fix build on current, if lld is lld7pi2019-01-081-0/+1
* biology/groopm fails to build with python3antoine2019-01-071-1/+1
* Update dns/libidn2 to 2.1.0sunpoet2019-01-072-0/+2
* Update science/hdf5 to 1.10.4sunpoet2019-01-061-1/+1
* biology/ncbi-blast+: Upgrade to 2.8.1jwb2019-01-024-32/+244
* biology/diamond: Update to version 0.9.24jrm2019-01-014-27/+12
* biology/iqtree: switch to outsource cmake buildjrm2018-12-281-2/+2
* Update math/eigen3 to 3.3.7tcberner2018-12-261-0/+1
* Change cmake default behaviour to outsource.tcberner2018-12-268-8/+8
* biology/iqtree: Update to version 1.6.9jrm2018-12-232-5/+4
* - Update to 1.73wen2018-12-222-5/+4
* Remove expired ports:rene2018-12-214-57/+0
* biology/gff2ps: update 0.98d to 0.98legypcio2018-12-202-5/+5
* biology/diamond: Update to 0.9.23 plus fixes after releasejrm2018-12-183-10/+11
* 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
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