aboutsummaryrefslogtreecommitdiffstats
path: root/biology
Commit message (Expand)AuthorAgeFilesLines
* 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 0.13yuri2017-11-062-6/+8
* biology/diamond: Update to 0.9.11jrm2017-11-033-10/+14
* biology/molden: chase another intransparent upstream distfile upgrade.jmd2017-11-012-4/+4
* - Fix installing scripts and support binarieswen2017-10-304-8/+39
* Update biology/py-pysam to 0.12.0.1tcberner2017-10-262-4/+4
* biology/htslib biology/bcftools biology/samtools: Update to 1.6pizzamig2017-10-2525-897/+171
* biology/iqtree: Add EXAMPLES option and fix mess with installation ofjrm2017-10-221-1/+13
* New port, biology/iqtree: Efficient phylogenomic softwarejrm2017-10-224-0/+43
* Mark as broken ports with no public distfilesbapt2017-10-136-1/+10
* Remove dead master sitesbapt2017-10-132-2/+3
* biology/molden: unbreak by chasing latest intransparent distfile update.jmd2017-09-282-4/+4
* devel/boost-*: update to 1.65.1jbeich2017-09-251-1/+1
* devel/boost-*: enable C++11 featuresjbeich2017-09-251-1/+1
* biology/ssaha: unbreak with gcc7jbeich2017-09-251-0/+9
* Remove USES=execinfo.mat2017-09-222-2/+2
* Update tbb to 2018 and bump dependent ports' revisionsmartymac2017-09-171-1/+1
* Update to 1.007002sunpoet2017-09-163-23/+5
* Add p5-Bio-FeatureIO 1.6.905sunpoet2017-09-165-0/+67
* Fix license information for portgs that use "the same license as Perl".mat2017-09-1510-10/+10
* - Update to 1.007002wen2017-09-133-15/+4
* Bump PORTREVISION for ports depending on the canonical version of GCCgerald2017-09-1115-15/+15
* Update to 3.3.20170530sunpoet2017-09-042-3/+5
* Remove expired ports:rene2017-08-235-87/+0
* Update GNUstep core libraries.theraven2017-08-211-1/+1
* - update to 1.70wen2017-08-182-4/+4
* biology/diamond: Update to version 0.9.10jrm2017-08-162-4/+4
* - Update to 1.53wen2017-07-232-4/+4
* Deprecate ports BROKEN for more than 6 monthsantoine2017-07-221-0/+2
* biology/seaview: Update version 4.6.1=>4.6.2bofh2017-07-222-4/+4
* Chase next distfile update. Upstream contacted whether we would be allowed to...jmd2017-07-142-4/+4
* biology/molden: Unbreak by chasing their latest opaque update to the distribu...jmd2017-07-122-7/+5
* Update math/gsl to 2.4tcberner2017-07-041-1/+1
* biology/diamond: Update to version 0.9.9jrm2017-07-042-4/+4
* Update devel/readline to 7.0 patch 3sunpoet2017-06-271-1/+1
* Begin deorbit burn of ia64. We have not attempted to build packages forlinimon2017-06-251-1/+1
* Mark BROKEN.mat2017-06-221-0/+2
* biology/diamond: Update to version 0.9.8jrm2017-06-162-4/+4
* - Update WWWamdmi32017-06-102-8/+7
* - Update to 0.11.2.2wen2017-06-102-4/+4
* Previous commit unbroke the port.linimon2017-06-031-2/+0
* biology/diamond: Update to version 0.9.4jrm2017-06-032-4/+4
* Remove outdated PERL_LEVEL checksunpoet2017-06-021-8/+2
* Remove outdated PERL_LEVEL checksunpoet2017-06-021-8/+2
* Update WWWsunpoet2017-05-301-1/+1
* biology/diamond: Update to version 0.9.3jrm2017-05-292-4/+4
* Mark some ports failing on armv6, for errors classified as "clang".linimon2017-05-271-0/+2
* Mark some ports failing on armv6, for errors classified as "???".linimon2017-05-272-3/+6
* biology/molden: Chase recent upstream change of molden distfile.jmd2017-05-242-4/+4
* - Update to 0.11.2.1joneum2017-05-242-5/+5
* biology/diamond: Update to version 0.9.1jrm2017-05-232-6/+6
* Revision bump of all ports with USE_GL after consolidation of mesa-libsrezny2017-05-233-3/+3
* It is possible that r441426 will fix the build problem on armv6. Givelinimon2017-05-221-1/+0
* Mark some ports failing on power64. In cases where the error messagelinimon2017-05-221-0/+2
* Mark BROKEN: checksum and size mismatchantoine2017-05-201-0/+2
* - Update to 5.15.0wen2017-05-183-3/+14
* Mark some ports failing on power64. In cases where the error messagelinimon2017-05-135-3/+6
* - Update to 0.11.1miwi2017-05-082-4/+4
* - Update to 1.5.1miwi2017-05-072-6/+4
* bx-python is a python library and associated set of scripts to allow for rapidmiwi2017-05-064-0/+47
* pysam is a lightweight wrapper of the htslib C-API and provides facilities tomiwi2017-05-065-0/+47
* - Update to 1.69wen2017-05-032-4/+4
* devel/boost-*: update to 1.64.0jbeich2017-05-021-1/+1
* Update math/gsl to 2.3tcberner2017-05-021-0/+1
* Provide error messages for some ports failing on aarch64, and, in alinimon2017-05-022-0/+5
* 2017-04-30 devel/stormlib-ghost++: Unfetchable for more than six months (goog...ler2017-04-305-79/+0
* biology/py-biom-format: Update to version 2.1.6jrm2017-04-292-4/+5
* - Fix shebangsmiwi2017-04-221-2/+3
* - Fix shebangsmiwi2017-04-221-3/+4
* - Fix shebangsamdmi32017-04-221-3/+7
* biology/diamond: Update to version 0.8.38jrm2017-04-212-6/+5
* biology/seaview: Update version 4.6=>4.6.1bofh2017-04-122-4/+5
* biology/diamond: Update to version 0.8.37jrm2017-04-022-5/+5
* Bump PORTREVISIONs for ports depending on the canonical version of GCC andgerald2017-04-0116-11/+16
* Update devel/tbb to 2017.5martymac2017-03-071-0/+1
* Mark the remaining ports depending on Google Code as DEPRECATED, with anmat2017-03-041-0/+2
* - Update to 1.42wen2017-03-012-4/+4
* Fix USE_GITHUB's GH_TAGNAME usage.mat2017-02-282-5/+5
* biology/plinkseq: unbreak with clang 4.0jbeich2017-02-272-0/+12
* biology/bowtie2: update to 2.3.0jbeich2017-02-274-6/+48
* Mark a few more ports that create large logfiles broken on armv6.linimon2017-02-261-0/+2
* Mark various ports as broken on armv6: invokes x86 asm.linimon2017-02-262-0/+2
* - Update to 1.14.9danilo2017-02-253-6/+12
* Move -fPIC to where Linux puts it so it is limited to a single library.tijl2017-02-142-4/+2
* biology/diamond: Update to version 0.8.36.jrm2017-02-122-4/+4
* biology/molden: Unbreak port, regenerate checksums, increment PORTREVISION.jmd2017-02-112-7/+5
* Add -fPIC to various ports to enable them to build on armv6.linimon2017-02-101-8/+3
* - Mark BROKEN: does not fetch, size/checksum mismatchamdmi32017-02-071-0/+2
* Update to 1.5.1sunpoet2017-02-072-9/+8
* biology/diamond: Update to version 0.8.35.jrm2017-02-062-5/+5
* Move devel/rubygem-bio to biology/rubygem-biosunpoet2017-02-054-0/+36
* Bump PORTREVISION for ports affected by the fix the last commit.mat2017-02-013-1/+3
* Mark various ports broken on aarch64 and armv6.linimon2017-01-311-0/+2
* biology/diamond: Update to version 0.8.34.jrm2017-01-232-4/+4
* Update WWW: SF redirects to https://sourceforge.net/projects/<PROJECT_NAME>/sunpoet2017-01-213-3/+3
* biology/diamond: Update to version 0.8.32.jrm2017-01-162-4/+4
* biology/diamond: Update to version 0.8.31.jrm2017-01-132-4/+4
* - Remove always-true/false conditions after FreeBSD 9, 10.1, 10.2 EOLamdmi32017-01-092-15/+3
* devel/boost-*: update to 1.63.0jbeich2017-01-061-1/+1
* Never set WRKSRC when using USE_GITHUB.mat2017-01-042-4/+0
* Assume "pkg-config zlib" works after 9.x reached EOLjbeich2017-01-041-3/+0
* Remove BROKEN_FreeBSD_9sunpoet2017-01-012-3/+0
* biology/diamond: Update to version 0.8.30jrm2016-12-312-4/+4
* biology/ncbi-blast+: Add MAKE_JOBS_UNSAFEjrm2016-12-231-0/+2
* - Update to 1.007001sunpoet2016-12-212-4/+4
* biology/bowtie2: Update to version 2.2.9jrm2016-12-212-14/+18
* biology/cd-hit: Update to bug-fix release 4.6.6jrm2016-12-212-5/+4
* biology/jellyfish: Update to version 2.2.6jrm2016-12-203-54/+56
* - Update *_DEPENDS: Bio::Coordinate family has been moved from biology/p5-Bio...sunpoet2016-12-191-2/+4
* - Add p5-Bio-Coordinate 1.007001sunpoet2016-12-195-0/+58
* - Update to 1.007000sunpoet2016-12-194-20/+29
* - Update to 1.007001sunpoet2016-12-196-383/+180
* - Update to 2.5.0wen2016-12-195-68/+190
* - Update to 2.40sunpoet2016-12-183-10/+22
* - Move biology/p5-bioperl-run to biology/p5-BioPerl-Runsunpoet2016-12-186-8/+10
* - Add LICENSE_FILEsunpoet2016-12-181-2/+5
* - Add LICENSEsunpoet2016-12-181-4/+8
* - Add LICENSEsunpoet2016-12-181-1/+7
* - Move biology/p5-bioperl to biology/p5-BioPerlsunpoet2016-12-187-9/+7
* biology/diamond: Update to version 0.8.29jrm2016-12-182-4/+4
* biology/protomol: Support build with C++11 (taken from dports)marino2016-12-185-0/+48
* biology/blat: Fix build on DF (taken from dports)marino2016-12-181-0/+14
* biology/lamarc: Fix build on DF (taken from dports)marino2016-12-181-0/+11
* biology/chemeq: fix build on GCC (taken from dports)marino2016-12-181-0/+11
* Remove libintl.so.9 compatibility link that was added in r374303 totijl2016-12-093-2/+3
* Remove libjpeg.so.11 compatibility link that was added in r374303 totijl2016-12-091-0/+1
* Bump PORTREVISIONS for ports depending on the canonical version of GCC andgerald2016-12-077-5/+7
* biology/molden: distfile was updated in xwin.cpi2016-12-042-4/+4
* Do not use post-stage. Use post-install instead.mat2016-12-021-1/+1
* biology/njplot: Add site in MASTER_SITES because package builders arejrm2016-11-281-2/+4
* biology/diamond: Update to version 0.8.28jrm2016-11-282-5/+6
* Fixup USE_GITHUB usage.mat2016-11-262-3/+3
* Replace USE_GCC=4.9+ by USE_GCC=yes, now that lang/gcc and the defaultgerald2016-11-261-1/+1
* devel/boost-*: update to 1.62.0jbeich2016-11-231-0/+1
* - Remove unnecessary USES=shebangfixsunpoet2016-11-211-4/+8
* Bump PORTREVISIONS for ports depending on the canonical version of GCC andgerald2016-11-205-2/+5
* biology/avida: Fix ncurses from ports supportmarino2016-11-191-1/+3
* biology/njplot: Revive and update to version 2.4jrm2016-11-165-0/+109
* Mark various leaf ports broken on aarch64, and, where appropriate, otherlinimon2016-11-114-2/+8
* Attempt to fix build on non-x86 archs.linimon2016-11-111-3/+5
* biology/seqtools: update 4.43.0 -> 4.44.1pi2016-11-113-4/+14
* biology/molden: add missing LICENSE_NAMEpi2016-11-101-1/+2
* biology/molden: fix distinfo, set LICENSEpi2016-11-102-7/+11
* The 64-bit arm arch is actually spelled 'aarch64', not 'arm64'.linimon2016-11-093-3/+3
* Mark as broken on arm64.linimon2016-11-081-0/+2
* Mark broken on all tier-2 archs.linimon2016-11-081-0/+3
* Mark broken on the rest of the tier-2 archs: invokes x86 asm.linimon2016-11-081-1/+4
* biology/diamond: Update to version 0.8.26jrm2016-11-062-4/+4
* Cleanup no longer needed CHMOD usage after r424898.mat2016-11-034-12/+5
* - Mark it BROKENwen2016-10-281-1/+3
* Use USES=pathfix where applicable.mat2016-10-214-21/+11
* ${RM} already has -f.mat2016-10-213-3/+3
* biology/diamond: update to version 0.8.24jrm2016-10-172-4/+4
* biology/diamond: update to version 0.8.23jrm2016-10-102-4/+4
* Mark BROKEN: unfetchable, size mismatchantoine2016-10-011-0/+1
generated by cgit (git 2.34.1) at 2024-12-18 02:58:03 +0800