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generated by cgit (git 2.34.1) at 2024-12-13 08:55:24 +0800
+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