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* 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
* biology/blat: Fix build with non-base SSLmarino2016-10-011-4/+4
* Update PORTREVISION and dinstinfo due to upstream tarball changejrm2016-09-302-3/+4
* biology/paml: update to version 4.9c and various improvementsjrm2016-09-284-33/+48
* Update email address to jrm@FreeBSD.org for ports that I maintainjrm2016-09-243-5/+3
* - Update to 1.68wen2016-09-232-3/+4
* - Update biology/seqan and bilogy/seqan-apps to version 2.2.0 [1]pawel2016-09-156-28/+39
* GOOGLE_CODE has gone away.mat2016-09-141-0/+2
* - Update to 0.8.22amdmi32016-09-142-4/+4
* biology/ncbi-blast+: Remove redundant LIB_DEPENDS (bz2 libary)marino2016-09-111-3/+2
* - Update to 1.72wen2016-09-112-4/+4
* Most commonly used build systems support silent builds, when theyamdmi32016-09-101-1/+1
* - Make configure script handle --disable-silent-rules gracefullyamdmi32016-09-061-1/+1
* - Update to 0.8.20wen2016-09-062-4/+4
* - Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk withtijl2016-09-062-4/+3
* biology/molden: 5.4 -> 5.7pi2016-08-262-6/+4
* Update to version 0.8.19pawel2016-08-262-4/+4
* - Mark BROKEN: does not fetch (distfile was removed from ftp)amdmi32016-08-221-0/+2
* biology/bedtools is not jobs safemarino2016-08-221-0/+2
* - Switch to options helpersamdmi32016-08-183-16/+11
* Update biology/diamond to 0.8.18.brd2016-08-152-4/+4
* - Update to 1.9 [1]wen2016-08-082-10/+8
* Update to version 0.8.17pawel2016-08-062-5/+5
* biology/seqtools: 4.42.1 -> 4.43.0pi2016-07-313-17/+227
* Update to upstream release 0.8.16riggs2016-07-252-4/+4
* Cleanup $() variables in ports Makefiles.mat2016-07-201-1/+1
* - update libgd to 2.2.2dinoex2016-07-201-1/+1
* When there is a do-install target, do not use a post-install target, domat2016-07-193-4/+5
* Trim excess tabs, no-op changepawel2016-07-151-13/+13
* Update to version 0.8.14pawel2016-07-152-4/+4
* - Update to 0.8.11amdmi32016-07-072-5/+5
* Remove expired ports without open PRs:rene2016-07-057-161/+0
* - LICENSEamdmi32016-07-022-10/+22
* biology/diamond: update 0.8.6 -> 0.8.9junovitch2016-06-302-4/+4
* - Add missing dependency, fixing buildamdmi32016-06-241-1/+5
* - Switch to options helpersamdmi32016-06-212-7/+11
* biology/diamond: update to 0.8.6rm2016-06-182-4/+4
* - Fix run-time dependency issuesolivierd2016-06-111-2/+13
* biology/seaview: Update version 4.5.4.8=>4.6bofh2016-06-102-7/+4
* Update to 0.8.5matthew2016-06-093-34/+18
* - Update to 1.35wen2016-06-082-3/+4
* Remove unneeded usage of:mat2016-06-061-2/+1
* Deprecate ports broken for more than 6 monthsantoine2016-06-042-0/+4
* - Do install cmake and pkgconfig modulesamdmi32016-05-282-3/+8
* biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1pi2016-05-278-20/+23
* Remove useless WRKSRC definitions.mat2016-05-251-2/+0
* - Fix trailing whitespace in pkg-messagesamdmi32016-05-196-12/+12
* - Fix trailing whitespace in pkg-descrs, categories [a-f]*amdmi32016-05-1921-36/+36
* Fix DEPENDSantoine2016-05-191-2/+2
* - Convert to USES=mysqlamdmi32016-05-171-8/+4
* - 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
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