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it/cgit.cgi/freebsd-ports-graphics/commit/biology?h=master&id=2753d409e921691914ff436bfc32fbfbbda9d11f'>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 * biology/py-pysam: Update to 0.13yuri2017-11-06