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* - Fix run-time dependency issuesOlivier Duchateau2016-06-111-2/+13
* biology/seaview: Update version 4.5.4.8=>4.6Muhammad Moinur Rahman2016-06-102-7/+4
* Update to 0.8.5Matthew Seaman2016-06-093-34/+18
* - Update to 1.35Wen Heping2016-06-082-3/+4
* Remove unneeded usage of:Mathieu Arnold2016-06-061-2/+1
* Deprecate ports broken for more than 6 monthsAntoine Brodin2016-06-042-0/+4
* - Do install cmake and pkgconfig modulesDmitry Marakasov2016-05-282-3/+8
* biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1Kurt Jaeger2016-05-278-20/+23
* Remove useless WRKSRC definitions.Mathieu Arnold2016-05-251-2/+0
* - Fix trailing whitespace in pkg-messagesDmitry Marakasov2016-05-196-12/+12
* - Fix trailing whitespace in pkg-descrs, categories [a-f]*Dmitry Marakasov2016-05-1921-36/+36
* Fix DEPENDSAntoine Brodin2016-05-191-2/+2
* - Convert to USES=mysqlDmitry Marakasov2016-05-171-8/+4
* - Update to 4.9aDmitry Marakasov2016-05-172-4/+7
* biology/bowtie2: 2.2.7 -> 2.2.8Kurt Jaeger2016-05-142-3/+3
* Prevent collision with getline(3)Baptiste Daroussin2016-05-141-0/+300
* Prevent collision with getline(3)Baptiste Daroussin2016-05-141-0/+291
* Prevent collision with getline(3)Baptiste Daroussin2016-05-124-6/+27
* biology/seqan: update 1.3.1 -> 2.1.1Jason Unovitch2016-05-1012-1915/+3706
* New port: biology/seqan-appsJason Unovitch2016-05-105-0/+220
* Add final slash in WWW entryOlivier Duchateau2016-05-101-1/+1
* The BIOM file format (canonically pronounced biome) is designed to be aOlivier Duchateau2016-05-104-0/+48
* During the exp-run in bug 208158, it was found that biology/ugene givesDimitry Andric2016-05-084-0/+36
* DNA query sequences against a protein reference database (BLASTP and BLASTXWen Heping2016-05-065-0/+71
* - Update to 1.14.8Danilo Egea Gondolfo2016-05-013-4/+4
* biology/seqtools: 4.41.1 -> 4.42.1Kurt Jaeger2016-04-232-5/+5
* many ports: mark broken on powerpc64Steve Wills2016-04-221-0/+2
* - Switch to options helpersDmitry Marakasov2016-04-173-16/+17
* - Update to 1.66Wen Heping2016-04-172-4/+3
* - Switch to options helpersDmitry Marakasov2016-04-161-3/+8
* Upgrade from 5.12.0 to 5.13.0. Release-announcement available here:Mikhail Teterin2016-04-163-4/+5
* Update to version 1.22.0, which now unfortunately requires Qt 5.x. AlsoAlexey Dokuchaev2016-04-149-36/+204
* - Add LICENSEDmitry Marakasov2016-04-101-1/+8
* Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.Mathieu Arnold2016-04-0138-148/+148
* - Update to 1.5.0Dmitry Marakasov2016-04-013-23/+11
* - Use more appropriate BROKEN instead of IGNOREDmitry Marakasov2016-03-301-4/+2
* - Update to 5.12.0Wen Heping2016-03-273-5/+7
* - Clarify LICENSEDmitry Marakasov2016-03-241-4/+3
* Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.Dmitry Marakasov2016-03-246-0/+146
* New port: biology/bowtie2.Raphael Kubo da Costa2016-03-236-0/+134
* New port: biology/slclust.Raphael Kubo da Costa2016-03-236-0/+85
* Trimmomatic performs a variety of useful trimming tasks for illuminaWen Heping2016-03-175-0/+41
* New port: biology/p5-transdecoderKurt Jaeger2016-03-175-0/+88
* biology/seqtools: 4.40.0 -> 4.41.1Kurt Jaeger2016-03-153-4/+6
* Always set the DEFAULT github DISTFILE with .tar.gz for EXTRACT_SUFX.Mathieu Arnold2016-03-081-2/+2
* New port: biology/bowtie.Raphael Kubo da Costa2016-03-056-0/+194
* New port: biology/vcftools.Raphael Kubo da Costa2016-02-275-0/+59
* - Update to 3.2.0Wen Heping2016-02-263-34/+62
* - Update to 1.14.7Danilo Egea Gondolfo2016-02-212-3/+3
* - Update to 1.34Wen Heping2016-02-122-3/+3
* biology/seqtools: 4.39.3 -> 4.40.0Kurt Jaeger2016-02-062-3/+3
* biology/mapm3: document ncurses rqmt (USES+=ncurses), respect LDFLAGSJohn Marino2016-02-021-0/+2
* biology/samtools: document ncurses requirement (USES+=ncurses)John Marino2016-02-021-1/+1
* biology/molden: updated distfile, take maintainerKurt Jaeger2016-01-212-4/+4
* Mark BROKEN: checksum and size mismatchAntoine Brodin2016-01-211-0/+1
* The bedtools utilities are a suite of tools for performing a wide range ofWen Heping2016-01-196-0/+135
* biology/molden: 5.0.7 -> 5.4Kurt Jaeger2016-01-195-192/+799
* mark ports that don't work with Ruby 2.3Steve Wills2016-01-171-0/+1
* Convert LICENSE= "GPLxx # or later" to "GPLxx+"Dmitry Marakasov2016-01-134-4/+4
* Add Public Domain support to ports license framework. You can now useDmitry Marakasov2016-01-121-3/+1
* Remove deprecated PLIST_DIRSTRY and also no longer needed PLIST_DIRSPawel Pekala2016-01-101-2/+0
* biology/crux is not jobs safeJohn Marino2015-12-311-0/+2
* biology/htslib: Replace FreeBSD-specific fix with a generic oneJohn Marino2015-12-291-5/+4
* Cleanup GH_* and variables order.Mathieu Arnold2015-12-293-3/+1
* biology/consed: undeprecate, it presumably builds fine but it is restricted.Rene Ladan2015-12-261-5/+1
* - Update to 7.266Wen Heping2015-12-255-42/+133
* biology/{bcftools,htslib,samtools}: update 1.2.x -> 1.3Jason Unovitch2015-12-2527-173/+930
* mark some of the ports that don't build on powerpc64 for meSteve Wills2015-12-144-0/+7
* - Update maintainer mail addressMartin Wilke2015-12-1112-23/+22
* - Update to 1.32Wen Heping2015-12-113-6/+8
* biology/seqtools: 4.39.2 -> 4.39.3Kurt Jaeger2015-12-052-3/+3
* biology/seqtools: 4.39.1 -> 4.39.2Kurt Jaeger2015-12-022-3/+3
* - Mark BROKEN: checksum mismatch:Dmitry Marakasov2015-11-291-0/+2
* Remove expired ports:Rene Ladan2015-11-2915-933/+0
* biology/platon: fix fetchingRuslan Makhmatkhanov2015-11-203-6/+4
* - Switch to options helpersDmitry Marakasov2015-11-191-1/+1
* biology/seqtools: Fix distinfo, WWWKurt Jaeger2015-11-182-3/+3
* biology/seqtools: 4.39.0 -> 4.39.1Kurt Jaeger2015-11-142-3/+3
* - Update to 1.14.6Danilo Egea Gondolfo2015-11-103-4/+4
* Mark a few ports BROKEN: unfetchableAntoine Brodin2015-11-091-0/+2
* biology/seqtools: 4.36 -> 4.39.0Kurt Jaeger2015-11-092-3/+3
* - Update to 1.14.5Danilo Egea Gondolfo2015-11-063-4/+4
* Fix ports that confused the meaning of WRKDIR and WRKSRC.Mathieu Arnold2015-11-051-5/+5
* biology/seaview: Broken, Does not fetch (checksum mismatch)John Marino2015-11-021-0/+2
* - Update to 2015.09.21Guido Falsi2015-10-285-25/+60
* Deprecate ports broken for more than 6 monthsAntoine Brodin2015-10-264-0/+8
* biology/seaview: Update version 4.5.4.7=>4.5.4.8Muhammad Moinur Rahman2015-10-202-3/+3
* - Update to 36.3.8Danilo Egea Gondolfo2015-10-162-4/+4
* - Add LICENSE_FILEDmitry Marakasov2015-10-151-1/+2
* - Pet portlintDmitry Marakasov2015-10-151-4/+5
* - Fix typoSunpoet Po-Chuan Hsieh2015-10-111-1/+1
* - Update to 1.14.4Danilo Egea Gondolfo2015-10-073-4/+4
* - Update to 1.14.3Danilo Egea Gondolfo2015-10-023-4/+4
* biology/seaview: Update version 4.5.4.6=>4.5.4.7Muhammad Moinur Rahman2015-10-012-4/+3
* biology/grappa: define license (GPLv2)Ruslan Makhmatkhanov2015-09-261-0/+2
* BWA is a program for aligning sequencing reads against a large referenceRuslan Makhmatkhanov2015-09-268-0/+84
* Fast indexing and retrieval of FASTA records from flat file data bases.Ruslan Makhmatkhanov2015-09-265-0/+85
* Simple and quick FastQ and FastA tool for file reading and conversion.Ruslan Makhmatkhanov2015-09-264-0/+39
* FastTree infers approximately-maximum-likelihood phylogenetic trees fromRuslan Makhmatkhanov2015-09-264-0/+41
* The FASTX-Toolkit is a collection of command line tools for Short-ReadsRuslan Makhmatkhanov2015-09-265-0/+57
* Gordon's text utilities.Ruslan Makhmatkhanov2015-09-265-0/+50
* Typos, whitespace and capitalization fixes (A-F).Jimmy Olgeni2015-09-211-1/+1
* - Use compiler:openmp instead of gccWen Heping2015-09-191-4/+1
* CD-HIT is a very widely used program for clustering and comparing protein orWen Heping2015-09-195-0/+81
* Make all GNUstep ports install into the System domain so that the Local domai...David Chisnall2015-09-192-66/+66
* - Update to 1.14.2Danilo Egea Gondolfo2015-09-173-4/+5
* Remove ansi version fo wxGTK 2.8 and only keep the unicode versionBaptiste Daroussin2015-09-172-1/+2
* biology/seaview: Update version 4.5.4.4=>4.5.4.6Muhammad Moinur Rahman2015-09-152-5/+5
* Make it so that the default Perl is always called perl5.Mathieu Arnold2015-09-145-72/+72
* Enfoce unicode version of wxGTKBaptiste Daroussin2015-09-141-0/+1
* - Update to 1.14.1Danilo Egea Gondolfo2015-09-143-5/+5
* - Add LICENSESunpoet Po-Chuan Hsieh2015-09-042-8/+8
* - Unbreak on PowerPC by using atomicops implementation for Linux and GCCAlexey Dokuchaev2015-09-022-12/+40
* - Do not falsely advertise that PowerPC build runs out of space and failsAlexey Dokuchaev2015-09-021-11/+5
* Unbreak the build on PowerPC (at least) by always using va_copy() macro forAlexey Dokuchaev2015-09-022-20/+7
* Unbreak the build on PowerPC, it had nothing to do with "error in pthreads":Alexey Dokuchaev2015-09-022-2/+20
* - Switch to options helpersDmitry Marakasov2015-09-021-6/+2
* Switch to USES=iconv:build.Raphael Kubo da Costa2015-08-251-1/+2
* Fix previous commit.Mathieu Arnold2015-08-191-1/+0
* Convert ports to use the options helpers in categories [abc]*, and minor fixes.Mathieu Arnold2015-08-197-41/+17
* biology/ugene: qt4-linguist -> qt4-linguisttoolsPhilip M. Gollucci2015-08-191-2/+3
* Remove UNIQUENAME and LATEST_LINK.Mathieu Arnold2015-08-171-2/+0
* biology/seqtools: 4.35 -> 4.36Kurt Jaeger2015-08-082-3/+3
* Fix build on mips by properly respecting compiler and flagsDmitry Marakasov2015-08-052-9/+20
* Update to 1.65.Mathieu Arnold2015-08-052-4/+4
* UnbreakAntoine Brodin2015-07-291-1/+1
* - Fix four cases of an obvious typo: LICENSE_FILES -> LICENSE_FILEAlexey Dokuchaev2015-07-251-2/+2
* - Update Unipro UGENE to version 1.17.0 (documentation was also rerolled)Alexey Dokuchaev2015-07-152-16/+11
* - Update to 1.14.0Danilo Egea Gondolfo2015-07-133-4/+5
* biology/seqtools: 4.34.1 -> 4.35Kurt Jaeger2015-07-072-5/+5
* After r390893, chmod u+w/u-w for stripping perl XS modules is unnecessary,Adam Weinberger2015-06-291-5/+2
* - Update optionsWen Heping2015-06-281-7/+1
* - Update to 3.6.11Wen Heping2015-06-282-15/+10
* Use BROKEN helpersBaptiste Daroussin2015-06-271-6/+2
* Use BROKEN helpersBaptiste Daroussin2015-06-271-5/+5
* - Add LICENSEDmitry Marakasov2015-06-251-1/+12
* Start removing MASTER_SITE_SUBDIR=CPAN:username where possible. TheAdam Weinberger2015-06-241-1/+0
* Convert to COPYTREE_SHAREBaptiste Daroussin2015-06-231-9/+6
* Convert to USES=jpegAntoine Brodin2015-06-231-1/+1
* - Fix shebangsDmitry Marakasov2015-06-111-1/+3
* New port: biology/bcftoolsKurt Jaeger2015-06-0610-0/+178
* - Strip binariesDmitry Marakasov2015-06-041-1/+2
* biology/mafft: update 7.149 -> 7.221Bartek Rutkowski2015-06-043-8/+7
* - Add NO_ARCHDmitry Marakasov2015-05-311-0/+1
* - Fix shebangsDmitry Marakasov2015-05-301-3/+9
* Update Unipro UGENE to version 1.16.2.Alexey Dokuchaev2015-05-283-3/+5
* Remove $FreeBSD$ from patches files in categories a-j.Mathieu Arnold2015-05-227-20/+0
* biology/seaview: Update version 4.5.4=>4.5.4.4Muhammad Moinur Rahman2015-05-222-3/+4
* - Update to 7.1.3Wen Heping2015-05-184-20/+22
* - Update to 3.6.9 and unbreakWen Heping2015-05-182-5/+3
* MASTER_SITES cleanup.Mathieu Arnold2015-05-143-7/+4
* - Update to 5.11.4Wen Heping2015-05-123-4/+10
* Cleanup DIST* variables.Mathieu Arnold2015-05-121-2/+1
* Reassign biology/ perl modules to perl@.Adam Weinberger2015-05-098-21/+22
* - Update to 36.3.7aWen Heping2015-05-073-6/+11
* biology/seqtools: 4.33 -> 4.34.1Kurt Jaeger2015-05-073-3/+7
* Update ports in the [bcd]* categories to not use GH_COMMIT.Mathieu Arnold2015-05-064-7/+4
* - UnbreakWen Heping2015-05-042-2/+11
* Mark BROKEN: fails to configureAntoine Brodin2015-04-281-0/+2
* biology/ncbi-blast+: Add additionl MASTER_SITE to unbreak fetchJohn Marino2015-04-251-3/+2
* ${ENV} does not exist, it is called ${SETENV}.Mathieu Arnold2015-04-131-1/+1
* biology/seaview: Unbreak -- it fetches fineJohn Marino2015-04-111-4/+1
* biology/platon: Upgrade from 05 MAR 2015 => 30 MAR 2015 to unbreakJohn Marino2015-04-112-6/+5
* biology/p5-Bio-ASN1-EntrezGene: bump PORTEPOCHJohn Marino2015-04-111-0/+1
* biology/p5-Bio-ASN1-EntrezGene: Upgrade 1.09 => 1.70 to unbreakJohn Marino2015-04-113-15/+15
* Update biology/paml to 4.8a and unbreak.Brad Davis2015-04-102-7/+5
* Convert bsd.gnustep.mk to USES=gnustepBaptiste Daroussin2015-04-091-4/+2
* Mark as broken unfetchable portsBaptiste Daroussin2015-04-0610-0/+18
* biology/ruby-bio: mark broken with ruby 2.2Steve Wills2015-04-031-1/+7
* - Remove deprecated optionDmitry Marakasov2015-04-021-9/+16
* biology/seqtools: 4.32 -> 4.33Kurt Jaeger2015-04-012-3/+3
* - Add LICENSESunpoet Po-Chuan Hsieh2015-03-291-4/+6
* Upgrade from 3.6.6 to 3.6.7. Be sure to not extract the zlibMikhail Teterin2015-03-252-3/+4
* 6 ports categories: Remove $PTHREAD_LIBSJohn Marino2015-03-253-10/+8
* biology/seaview: Update version 4.5.3.4=>4.5.4Muhammad Moinur Rahman2015-03-243-41/+5
* - Update to version 1.16.1Alexey Dokuchaev2015-03-233-8/+8
* biology/segan: Limit GCC to 4.8 while waiting for updateJohn Marino2015-03-211-1/+1
* For the new USE_GITHUB with only GH_TAGNAME set default DISTNAME toBryan Drewery2015-03-211-2/+2
* Convert to new USE_GITHUB.Mathieu Arnold2015-03-202-11/+4
* Fix packaging as a user (pkg already takes care of credentials)Baptiste Daroussin2015-03-191-2/+2
* - Simplify MASTER_SITESDmitry Marakasov2015-03-171-3/+9
* biology/seaview: UNBREAKMuhammad Moinur Rahman2015-03-163-15/+38
* Some OCD cleanups on some of the perl@ ports.Adam Weinberger2015-03-135-984/+976
* - Add empty directory to plistDmitry Marakasov2015-03-111-0/+1
* Update from 7.1.1 to 7.1.2.Mikhail Teterin2015-03-112-3/+3
* Unbreak by upgrading to March 5, 2015 "release" from upstream.Mikhail Teterin2015-03-095-106/+103
* Unbreak by updating from 7.0.1 to 7.1.1. Hopefully, the authors willMikhail Teterin2015-03-092-6/+4
* biology/samtools: update 1.1 -> 1.2Bartek Rutkowski2015-03-062-4/+5
* biology/htslib: update 1.1 -> 1.2.1Bartek Rutkowski2015-03-066-23/+45
* Add a run dependency used by update_blastdb.plTilman Keskinoz2015-03-061-1/+2
* - Update to 1.13.10Danilo Egea Gondolfo2015-03-043-4/+4
* Remove Authors from pkg-descrBaptiste Daroussin2015-03-031-1/+0
* Remove TEST dependency on p5-Test-Simple when the version in core isAdam Weinberger2015-02-271-1/+0
* Update Unipro UGENE to version 1.16.0 (documentation was also rerolled).Alexey Dokuchaev2015-02-243-9/+18
* Mark BROKEN: Fails to link, tries to use internal fltk symbolsAntoine Brodin2015-02-211-0/+2
* biology/seqtools: 4.31 -> 4.32Kurt Jaeger2015-02-122-3/+3
* Mark BROKEN: Checksum and size mismatchAntoine Brodin2015-01-311-0/+1
* - Update to 3.6.6Wen Heping2015-01-313-5/+5
* - Update to 1.13.9Danilo Egea Gondolfo2015-01-313-4/+4
* misc/otter & biology/ariadne: Not jobs safeJohn Marino2015-01-221-0/+2
* biology/py-biopython:Max Brazhnikov2015-01-201-3/+5
* Designatate 4 ports as unsafe for parallel buildingJohn Marino2015-01-201-0/+1
* - Pass maintainership to submitterWen Heping2015-01-191-1/+1
* - Simplify MakefileSunpoet Po-Chuan Hsieh2015-01-192-135/+130
* - Update to 1.13.8Danilo Egea Gondolfo2015-01-143-4/+4
* Mark BROKEN: UnfetchableAntoine Brodin2015-01-101-0/+1
* Update to version 1.15.1.Alexey Dokuchaev2015-01-063-10/+10
* biology/tinker: 6.2.6 -> 7.0.1Kurt Jaeger2015-01-046-65/+94
* - Convert USE_PYTHON -> USES leftovers missed in the previous commitsMarcus von Appen2015-01-041-1/+1
* Update to upstream version 36Thomas Zander2015-01-022-7/+6
* Remove expired ports:Rene Ladan2015-01-017-166/+0
* Fix PKGNAMEPREFIX of biology/ncbi-blast+, so that the resulting package isMichael Gmelin2014-12-311-1/+2
* Rename biology/ncbi-blast to biology/ncbi-blast+Michael Gmelin2014-12-315-2/+2
* - Update to 5.11.0Wen Heping2014-12-303-5/+28
* Convert to USES=autoreconfBaptiste Daroussin2014-12-291-2/+2
* Bump portrevision after png updateBaptiste Daroussin2014-12-263-1/+3
* Change libpng15.so to libpng.so in LIB_DEPENDS to prepare the upgradeAntoine Brodin2014-12-263-4/+4
* Change my non-FreeBSD MAINTAINER mail to bofh@Muhammad Moinur Rahman2014-12-241-1/+1
* Cleanup plistBaptiste Daroussin2014-12-217-8/+0
* - Upadate biology/mopac to version 1.15Pawel Pekala2014-12-176-41/+17
* Samtools implements various utilities for post-processing alignments in thePawel Pekala2014-12-168-0/+169
* HTSlib is an implementation of a unified C library for accessing common filePawel Pekala2014-12-156-0/+131
* biology/seqtools: 4.30 -> 4.31Kurt Jaeger2014-12-142-3/+3
* - Update to 2.39Wen Heping2014-12-072-4/+3
* - Update to 0.58Wen Heping2014-12-073-8/+9
* - Update to 3.6.5Wen Heping2014-12-063-6/+19
* Update to version 1.15.0.Alexey Dokuchaev2014-12-033-16/+34
* Change the way Perl modules are installed, update the default Perl to 5.18.Mathieu Arnold2014-11-2623-125/+125
* biology/seqtools: 4.29 -> 4.30Kurt Jaeger2014-11-042-4/+3
* - Update to version 3.696Pawel Pekala2014-11-023-30/+18
* Cleanup plistBaptiste Daroussin2014-10-2036-644/+0
* - Convert ports from benchmarks/ and biology/ to new USES=pythonMarcus von Appen2014-10-196-16/+10
* - Fix various distinfo errorsAlex Kozlov2014-10-161-1/+0
* biology/seqtools: 4.28 -> 4.29Kurt Jaeger2014-10-163-4/+3
* Update to version 1.14.2.Alexey Dokuchaev2014-10-133-4/+13
* - Update to 0.10Wen Heping2014-10-125-58/+32
* Fix pkg-plistRene Ladan2014-10-081-0/+3
* biology/boinc-simap: clean up pkg-plistRene Ladan2014-10-081-7/+5
* Add new port biology/ncbi-blastJohn Marino2014-10-075-0/+3961
* - Update to 2.6.0Sunpoet Po-Chuan Hsieh2014-10-041-1/+1
* - any version for RUN_DEPENDSDirk Meyer2014-09-211-2/+2
* - update RUN_DEPENDS for rubygems-dbiDirk Meyer2014-09-211-2/+2
* biology/boinc-simap: Deprecate, project shutting down on 2015-01-01Rene Ladan2014-09-201-0/+3
* devel/glib12 x11-toolkits/gtk12:Tijl Coosemans2014-09-131-1/+1
* Update the default version of GCC in the Ports Collection from GCC 4.7.4Gerald Pfeifer2014-09-1118-13/+18
* Fix MASTER_SITESAntoine Brodin2014-09-051-1/+1
* Second run at cleaning out non staged ports without pending PRBaptiste Daroussin2014-09-025-69/+0
* Remove non staged ports without pending PR from b*Baptiste Daroussin2014-09-0115-1973/+0
* - Update Unipro UGENE and documentation to version 1.14.0Alexey Dokuchaev2014-09-017-226/+71
* biology/crux: stage, modernize, add license (BSD[23]CLAUSE), cleanupsRene Ladan2014-08-274-46/+63
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