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* - Update to 4.9aamdmi32016-05-172-4/+7
* biology/bowtie2: 2.2.7 -> 2.2.8pi2016-05-142-3/+3
* Prevent collision with getline(3)bapt2016-05-141-0/+300
* Prevent collision with getline(3)bapt2016-05-141-0/+291
* Prevent collision with getline(3)bapt2016-05-124-6/+27
* biology/seqan: update 1.3.1 -> 2.1.1junovitch2016-05-1012-1915/+3706
* New port: biology/seqan-appsjunovitch2016-05-105-0/+220
* Add final slash in WWW entryolivierd2016-05-101-1/+1
* The BIOM file format (canonically pronounced biome) is designed to be aolivierd2016-05-104-0/+48
* During the exp-run in bug 208158, it was found that biology/ugene givesdim2016-05-084-0/+36
* DNA query sequences against a protein reference database (BLASTP and BLASTXwen2016-05-065-0/+71
* - Update to 1.14.8danilo2016-05-013-4/+4
* biology/seqtools: 4.41.1 -> 4.42.1pi2016-04-232-5/+5
* many ports: mark broken on powerpc64swills2016-04-221-0/+2
* - Switch to options helpersamdmi32016-04-173-16/+17
* - Update to 1.66wen2016-04-172-4/+3
* - Switch to options helpersamdmi32016-04-161-3/+8
* Upgrade from 5.12.0 to 5.13.0. Release-announcement available here:mi2016-04-163-4/+5
* Update to version 1.22.0, which now unfortunately requires Qt 5.x. Alsodanfe2016-04-149-36/+204
* - Add LICENSEamdmi32016-04-101-1/+8
* Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.mat2016-04-0138-148/+148
* - Update to 1.5.0amdmi32016-04-013-23/+11
* - Use more appropriate BROKEN instead of IGNOREamdmi32016-03-301-4/+2
* - Update to 5.12.0wen2016-03-273-5/+7
* - Clarify LICENSEamdmi32016-03-241-4/+3
* Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.amdmi32016-03-246-0/+146
* New port: biology/bowtie2.rakuco2016-03-236-0/+134
* New port: biology/slclust.rakuco2016-03-236-0/+85
* Trimmomatic performs a variety of useful trimming tasks for illuminawen2016-03-175-0/+41
* New port: biology/p5-transdecoderpi2016-03-175-0/+88
* biology/seqtools: 4.40.0 -> 4.41.1pi2016-03-153-4/+6
* Always set the DEFAULT github DISTFILE with .tar.gz for EXTRACT_SUFX.mat2016-03-081-2/+2
* New port: biology/bowtie.rakuco2016-03-056-0/+194
* New port: biology/vcftools.rakuco2016-02-275-0/+59
* - Update to 3.2.0wen2016-02-263-34/+62
* - Update to 1.14.7danilo2016-02-212-3/+3
* - Update to 1.34wen2016-02-122-3/+3
* biology/seqtools: 4.39.3 -> 4.40.0pi2016-02-062-3/+3
* biology/mapm3: document ncurses rqmt (USES+=ncurses), respect LDFLAGSmarino2016-02-021-0/+2
* biology/samtools: document ncurses requirement (USES+=ncurses)marino2016-02-021-1/+1
* biology/molden: updated distfile, take maintainerpi2016-01-212-4/+4
* Mark BROKEN: checksum and size mismatchantoine2016-01-211-0/+1
* The bedtools utilities are a suite of tools for performing a wide range ofwen2016-01-196-0/+135
* biology/molden: 5.0.7 -> 5.4pi2016-01-195-192/+799
* mark ports that don't work with Ruby 2.3swills2016-01-171-0/+1
* Convert LICENSE= "GPLxx # or later" to "GPLxx+"amdmi32016-01-134-4/+4
* Add Public Domain support to ports license framework. You can now useamdmi32016-01-121-3/+1
* Remove deprecated PLIST_DIRSTRY and also no longer needed PLIST_DIRSpawel2016-01-101-2/+0
* biology/crux is not jobs safemarino2015-12-311-0/+2
* biology/htslib: Replace FreeBSD-specific fix with a generic onemarino2015-12-291-5/+4
* Cleanup GH_* and variables order.mat2015-12-293-3/+1
* biology/consed: undeprecate, it presumably builds fine but it is restricted.rene2015-12-261-5/+1
* - Update to 7.266wen2015-12-255-42/+133
* biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3junovitch2015-12-2527-173/+930
* mark some of the ports that don't build on powerpc64 for meswills2015-12-144-0/+7
* - Update maintainer mail addressmiwi2015-12-1112-23/+22
* - Update to 1.32wen2015-12-113-6/+8
* biology/seqtools: 4.39.2 -> 4.39.3pi2015-12-052-3/+3
* biology/seqtools: 4.39.1 -> 4.39.2pi2015-12-022-3/+3
* - Mark BROKEN: checksum mismatch:amdmi32015-11-291-0/+2
* Remove expired ports:rene2015-11-2915-933/+0
* biology/platon: fix fetchingrm2015-11-203-6/+4
* - Switch to options helpersamdmi32015-11-191-1/+1
* biology/seqtools: Fix distinfo, WWWpi2015-11-182-3/+3
* biology/seqtools: 4.39.0 -> 4.39.1pi2015-11-142-3/+3
* - Update to 1.14.6danilo2015-11-103-4/+4
* Mark a few ports BROKEN: unfetchableantoine2015-11-091-0/+2
* biology/seqtools: 4.36 -> 4.39.0pi2015-11-092-3/+3
* - Update to 1.14.5danilo2015-11-063-4/+4
* Fix ports that confused the meaning of WRKDIR and WRKSRC.mat2015-11-051-5/+5
* biology/seaview: Broken, Does not fetch (checksum mismatch)marino2015-11-021-0/+2
* - Update to 2015.09.21madpilot2015-10-285-25/+60
* Deprecate ports broken for more than 6 monthsantoine2015-10-264-0/+8
* biology/seaview: Update version 4.5.4.7=>4.5.4.8bofh2015-10-202-3/+3
* - Update to 36.3.8danilo2015-10-162-4/+4
* - Add LICENSE_FILEamdmi32015-10-151-1/+2
* - Pet portlintamdmi32015-10-151-4/+5
* - Fix typosunpoet2015-10-111-1/+1
* - Update to 1.14.4danilo2015-10-073-4/+4
* - Update to 1.14.3danilo2015-10-023-4/+4
* biology/seaview: Update version 4.5.4.6=>4.5.4.7bofh2015-10-012-4/+3
* biology/grappa: define license (GPLv2)rm2015-09-261-0/+2
* BWA is a program for aligning sequencing reads against a large referencerm2015-09-268-0/+84
* Fast indexing and retrieval of FASTA records from flat file data bases.rm2015-09-265-0/+85
* Simple and quick FastQ and FastA tool for file reading and conversion.rm2015-09-264-0/+39
* FastTree infers approximately-maximum-likelihood phylogenetic trees fromrm2015-09-264-0/+41
* The FASTX-Toolkit is a collection of command line tools for Short-Readsrm2015-09-265-0/+57
* Gordon's text utilities.rm2015-09-265-0/+50
* Typos, whitespace and capitalization fixes (A-F).olgeni2015-09-211-1/+1
* - Use compiler:openmp instead of gccwen2015-09-191-4/+1
* CD-HIT is a very widely used program for clustering and comparing protein orwen2015-09-195-0/+81
* Make all GNUstep ports install into the System domain so that the Local domai...theraven2015-09-192-66/+66
* - Update to 1.14.2danilo2015-09-173-4/+5
* Remove ansi version fo wxGTK 2.8 and only keep the unicode versionbapt2015-09-172-1/+2
* biology/seaview: Update version 4.5.4.4=>4.5.4.6bofh2015-09-152-5/+5
* Make it so that the default Perl is always called perl5.mat2015-09-145-72/+72
* Enfoce unicode version of wxGTKbapt2015-09-141-0/+1
* - Update to 1.14.1danilo2015-09-143-5/+5
* - Add LICENSEsunpoet2015-09-042-8/+8
* - Unbreak on PowerPC by using atomicops implementation for Linux and GCCdanfe2015-09-022-12/+40
* - Do not falsely advertise that PowerPC build runs out of space and failsdanfe2015-09-021-11/+5
* Unbreak the build on PowerPC (at least) by always using va_copy() macro fordanfe2015-09-022-20/+7
* Unbreak the build on PowerPC, it had nothing to do with "error in pthreads":danfe2015-09-022-2/+20
* - Switch to options helpersamdmi32015-09-021-6/+2
* Switch to USES=iconv:build.rakuco2015-08-251-1/+2
* Fix previous commit.mat2015-08-191-1/+0
* Convert ports to use the options helpers in categories [abc]*, and minor fixes.mat2015-08-197-41/+17
* biology/ugene: qt4-linguist -> qt4-linguisttoolspgollucci2015-08-191-2/+3
* Remove UNIQUENAME and LATEST_LINK.mat2015-08-171-2/+0
* biology/seqtools: 4.35 -> 4.36pi2015-08-082-3/+3
* Fix build on mips by properly respecting compiler and flagsamdmi32015-08-052-9/+20
* Update to 1.65.mat2015-08-052-4/+4
* Unbreakantoine2015-07-291-1/+1
* - Fix four cases of an obvious typo: LICENSE_FILES -> LICENSE_FILEdanfe2015-07-251-2/+2
* - Update Unipro UGENE to version 1.17.0 (documentation was also rerolled)danfe2015-07-152-16/+11
* - Update to 1.14.0danilo2015-07-133-4/+5
* biology/seqtools: 4.34.1 -> 4.35pi2015-07-072-5/+5
* After r390893, chmod u+w/u-w for stripping perl XS modules is unnecessary,adamw2015-06-291-5/+2
* - Update optionswen2015-06-281-7/+1
* - Update to 3.6.11wen2015-06-282-15/+10
* Use BROKEN helpersbapt2015-06-271-6/+2
* Use BROKEN helpersbapt2015-06-271-5/+5
* - Add LICENSEamdmi32015-06-251-1/+12
* Start removing MASTER_SITE_SUBDIR=CPAN:username where possible. Theadamw2015-06-241-1/+0
* Convert to COPYTREE_SHAREbapt2015-06-231-9/+6
* Convert to USES=jpegantoine2015-06-231-1/+1
* - Fix shebangsamdmi32015-06-111-1/+3
* New port: biology/bcftoolspi2015-06-0610-0/+178
* - Strip binariesamdmi32015-06-041-1/+2
* biology/mafft: update 7.149 -> 7.221robak2015-06-043-8/+7
* - Add NO_ARCHamdmi32015-05-311-0/+1
* - Fix shebangsamdmi32015-05-301-3/+9
* Update Unipro UGENE to version 1.16.2.danfe2015-05-283-3/+5
* Remove $FreeBSD$ from patches files in categories a-j.mat2015-05-227-20/+0
* biology/seaview: Update version 4.5.4=>4.5.4.4bofh2015-05-222-3/+4
* - Update to 7.1.3wen2015-05-184-20/+22
* - Update to 3.6.9 and unbreakwen2015-05-182-5/+3
* MASTER_SITES cleanup.mat2015-05-143-7/+4
* - Update to 5.11.4wen2015-05-123-4/+10
* Cleanup DIST* variables.mat2015-05-121-2/+1
* Reassign biology/ perl modules to perl@.adamw2015-05-098-21/+22
* - Update to 36.3.7awen2015-05-073-6/+11
* biology/seqtools: 4.33 -> 4.34.1pi2015-05-073-3/+7
* Update ports in the [bcd]* categories to not use GH_COMMIT.mat2015-05-064-7/+4
* - Unbreakwen2015-05-042-2/+11
* Mark BROKEN: fails to configureantoine2015-04-281-0/+2
* biology/ncbi-blast+: Add additionl MASTER_SITE to unbreak fetchmarino2015-04-251-3/+2
* ${ENV} does not exist, it is called ${SETENV}.mat2015-04-131-1/+1
* biology/seaview: Unbreak -- it fetches finemarino2015-04-111-4/+1
* biology/platon: Upgrade from 05 MAR 2015 => 30 MAR 2015 to unbreakmarino2015-04-112-6/+5
* biology/p5-Bio-ASN1-EntrezGene: bump PORTEPOCHmarino2015-04-111-0/+1
* biology/p5-Bio-ASN1-EntrezGene: Upgrade 1.09 => 1.70 to unbreakmarino2015-04-113-15/+15
* Update biology/paml to 4.8a and unbreak.brd2015-04-102-7/+5
* Convert bsd.gnustep.mk to USES=gnustepbapt2015-04-091-4/+2
* Mark as broken unfetchable portsbapt2015-04-0610-0/+18
* biology/ruby-bio: mark broken with ruby 2.2swills2015-04-031-1/+7
* - Remove deprecated optionamdmi32015-04-021-9/+16
* biology/seqtools: 4.32 -> 4.33pi2015-04-012-3/+3
* - Add LICENSEsunpoet2015-03-291-4/+6
* Upgrade from 3.6.6 to 3.6.7. Be sure to not extract the zlibmi2015-03-252-3/+4
* 6 ports categories: Remove $PTHREAD_LIBSmarino2015-03-253-10/+8
* biology/seaview: Update version 4.5.3.4=>4.5.4bofh2015-03-243-41/+5
* - Update to version 1.16.1danfe2015-03-233-8/+8
* biology/segan: Limit GCC to 4.8 while waiting for updatemarino2015-03-211-1/+1
* For the new USE_GITHUB with only GH_TAGNAME set default DISTNAME tobdrewery2015-03-211-2/+2
* Convert to new USE_GITHUB.mat2015-03-202-11/+4
* Fix packaging as a user (pkg already takes care of credentials)bapt2015-03-191-2/+2
* - Simplify MASTER_SITESamdmi32015-03-171-3/+9
* biology/seaview: UNBREAKbofh2015-03-163-15/+38
* Some OCD cleanups on some of the perl@ ports.adamw2015-03-135-984/+976
* - Add empty directory to plistamdmi32015-03-111-0/+1
* Update from 7.1.1 to 7.1.2.mi2015-03-112-3/+3
* Unbreak by upgrading to March 5, 2015 "release" from upstream.mi2015-03-095-106/+103
* Unbreak by updating from 7.0.1 to 7.1.1. Hopefully, the authors willmi2015-03-092-6/+4
* biology/samtools: update 1.1 -> 1.2robak2015-03-062-4/+5
* biology/htslib: update 1.1 -> 1.2.1robak2015-03-066-23/+45
* Add a run dependency used by update_blastdb.plarved2015-03-061-1/+2
* - Update to 1.13.10danilo2015-03-043-4/+4
* Remove Authors from pkg-descrbapt2015-03-031-1/+0
* Remove TEST dependency on p5-Test-Simple when the version in core isadamw2015-02-271-1/+0
* Update Unipro UGENE to version 1.16.0 (documentation was also rerolled).danfe2015-02-243-9/+18
* Mark BROKEN: Fails to link, tries to use internal fltk symbolsantoine2015-02-211-0/+2
* biology/seqtools: 4.31 -> 4.32pi2015-02-122-3/+3
* Mark BROKEN: Checksum and size mismatchantoine2015-01-311-0/+1
* - Update to 3.6.6wen2015-01-313-5/+5
* - Update to 1.13.9danilo2015-01-313-4/+4
* misc/otter & biology/ariadne: Not jobs safemarino2015-01-221-0/+2
* biology/py-biopython:makc2015-01-201-3/+5
* Designatate 4 ports as unsafe for parallel buildingmarino2015-01-201-0/+1
* - Pass maintainership to submitterwen2015-01-191-1/+1
* - Simplify Makefilesunpoet2015-01-192-135/+130
* - Update to 1.13.8danilo2015-01-143-4/+4
* Mark BROKEN: Unfetchableantoine2015-01-101-0/+1
* Update to version 1.15.1.danfe2015-01-063-10/+10
* biology/tinker: 6.2.6 -> 7.0.1pi2015-01-046-65/+94
* - Convert USE_PYTHON -> USES leftovers missed in the previous commitsmva2015-01-041-1/+1
* Update to upstream version 36riggs2015-01-022-7/+6
* Remove expired ports:rene2015-01-017-166/+0
* Fix PKGNAMEPREFIX of biology/ncbi-blast+, so that the resulting package isgrembo2014-12-311-1/+2
* Rename biology/ncbi-blast to biology/ncbi-blast+grembo2014-12-315-2/+2
* - Update to 5.11.0wen2014-12-303-5/+28
* Convert to USES=autoreconfbapt2014-12-291-2/+2
* Bump portrevision after png updatebapt2014-12-263-1/+3
* Change libpng15.so to libpng.so in LIB_DEPENDS to prepare the upgradeantoine2014-12-263-4/+4
* Change my non-FreeBSD MAINTAINER mail to bofh@bofh2014-12-241-1/+1
* Cleanup plistbapt2014-12-217-8/+0
* - Upadate biology/mopac to version 1.15pawel2014-12-176-41/+17
* Samtools implements various utilities for post-processing alignments in thepawel2014-12-168-0/+169
* HTSlib is an implementation of a unified C library for accessing common filepawel2014-12-156-0/+131
* biology/seqtools: 4.30 -> 4.31pi2014-12-142-3/+3
* - Update to 2.39wen2014-12-072-4/+3
* - Update to 0.58wen2014-12-073-8/+9
* - Update to 3.6.5wen2014-12-063-6/+19
* Update to version 1.15.0.danfe2014-12-033-16/+34
* Change the way Perl modules are installed, update the default Perl to 5.18.mat2014-11-2623-125/+125
* biology/seqtools: 4.29 -> 4.30pi2014-11-042-4/+3
* - Update to version 3.696pawel2014-11-023-30/+18
* Cleanup plistbapt2014-10-2036-644/+0
* - Convert ports from benchmarks/ and biology/ to new USES=pythonmva2014-10-196-16/+10
* - Fix various distinfo errorsak2014-10-161-1/+0
* biology/seqtools: 4.28 -> 4.29pi2014-10-163-4/+3
* Update to version 1.14.2.danfe2014-10-133-4/+13
* - Update to 0.10wen2014-10-125-58/+32
* Fix pkg-plistrene2014-10-081-0/+3
* biology/boinc-simap: clean up pkg-plistrene2014-10-081-7/+5
* Add new port biology/ncbi-blastmarino2014-10-075-0/+3961
* - Update to 2.6.0sunpoet2014-10-041-1/+1
* - any version for RUN_DEPENDSdinoex2014-09-211-2/+2
* - update RUN_DEPENDS for rubygems-dbidinoex2014-09-211-2/+2
* biology/boinc-simap: Deprecate, project shutting down on 2015-01-01rene2014-09-201-0/+3
* devel/glib12 x11-toolkits/gtk12:tijl2014-09-131-1/+1
* Update the default version of GCC in the Ports Collection from GCC 4.7.4gerald2014-09-1118-13/+18
* Fix MASTER_SITESantoine2014-09-051-1/+1
* Second run at cleaning out non staged ports without pending PRbapt2014-09-025-69/+0
* Remove non staged ports without pending PR from b*bapt2014-09-0115-1973/+0
* - Update Unipro UGENE and documentation to version 1.14.0danfe2014-09-017-226/+71
* biology/crux: stage, modernize, add license (BSD[23]CLAUSE), cleanupsrene2014-08-274-46/+63
* - Stagifyamdmi32014-08-268-3/+124
* update ports:pi2014-08-2431-1187/+735
* Fix build. Hopefully it doesn't break the app.adamw2014-08-221-0/+11
* Fix build on -current by un-clobbering LDFLAGS. Also, don'tadamw2014-08-162-4/+13
* - Update to 5.10.2wen2014-08-104-270/+232
* Convert the Python framework bits to USES=python.mva2014-08-091-2/+2
* - Switch to USES=libtool, drop .la filesamdmi32014-08-072-4/+4
* USES=execinfobapt2014-08-052-6/+2
* biology/p5-bioperl-run: 1.6.1 -> 1.6.901, unbreak, stagifypi2014-08-045-217/+296
* biology/p5-bioperl: fix pkg-descr sidenote linkpi2014-08-041-1/+1
* Add a DOCS option.adamw2014-08-042-5/+7
* biology/seqtools: 4.27 -> 4.28pi2014-07-312-3/+3
* Convert a bunch of EXTRACT_SUFX=... into USES=tar:...adamw2014-07-308-16/+8
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