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* Bump PORTREVISION for ports affected by the fix the last commit.Mathieu Arnold2017-02-013-1/+3
* Mark various ports broken on aarch64 and armv6.Mark Linimon2017-01-311-0/+2
* biology/diamond: Update to version 0.8.34.Joseph Mingrone2017-01-232-4/+4
* Update WWW: SF redirects to https://sourceforge.net/projects/<PROJECT_NAME>/Sunpoet Po-Chuan Hsieh2017-01-213-3/+3
* biology/diamond: Update to version 0.8.32.Joseph Mingrone2017-01-162-4/+4
* biology/diamond: Update to version 0.8.31.Joseph Mingrone2017-01-132-4/+4
* - Remove always-true/false conditions after FreeBSD 9, 10.1, 10.2 EOLDmitry Marakasov2017-01-092-15/+3
* devel/boost-*: update to 1.63.0Jan Beich2017-01-061-1/+1
* Never set WRKSRC when using USE_GITHUB.Mathieu Arnold2017-01-042-4/+0
* Assume "pkg-config zlib" works after 9.x reached EOLJan Beich2017-01-041-3/+0
* Remove BROKEN_FreeBSD_9Sunpoet Po-Chuan Hsieh2017-01-012-3/+0
* biology/diamond: Update to version 0.8.30Joseph Mingrone2016-12-312-4/+4
* biology/ncbi-blast+: Add MAKE_JOBS_UNSAFEJoseph Mingrone2016-12-231-0/+2
* - Update to 1.007001Sunpoet Po-Chuan Hsieh2016-12-212-4/+4
* biology/bowtie2: Update to version 2.2.9Joseph Mingrone2016-12-212-14/+18
* biology/cd-hit: Update to bug-fix release 4.6.6Joseph Mingrone2016-12-212-5/+4
* biology/jellyfish: Update to version 2.2.6Joseph Mingrone2016-12-203-54/+56
* - Update *_DEPENDS: Bio::Coordinate family has been moved from biology/p5-Bio...Sunpoet Po-Chuan Hsieh2016-12-191-2/+4
* - Add p5-Bio-Coordinate 1.007001Sunpoet Po-Chuan Hsieh2016-12-195-0/+58
* - Update to 1.007000Sunpoet Po-Chuan Hsieh2016-12-194-20/+29
* - Update to 1.007001Sunpoet Po-Chuan Hsieh2016-12-196-383/+180
* - Update to 2.5.0Wen Heping2016-12-195-68/+190
* - Update to 2.40Sunpoet Po-Chuan Hsieh2016-12-183-10/+22
* - Move biology/p5-bioperl-run to biology/p5-BioPerl-RunSunpoet Po-Chuan Hsieh2016-12-186-8/+10
* - Add LICENSE_FILESunpoet Po-Chuan Hsieh2016-12-181-2/+5
* - Add LICENSESunpoet Po-Chuan Hsieh2016-12-181-4/+8
* - Add LICENSESunpoet Po-Chuan Hsieh2016-12-181-1/+7
* - Move biology/p5-bioperl to biology/p5-BioPerlSunpoet Po-Chuan Hsieh2016-12-187-9/+7
* biology/diamond: Update to version 0.8.29Joseph Mingrone2016-12-182-4/+4
* biology/protomol: Support build with C++11 (taken from dports)John Marino2016-12-185-0/+48
* biology/blat: Fix build on DF (taken from dports)John Marino2016-12-181-0/+14
* biology/lamarc: Fix build on DF (taken from dports)John Marino2016-12-181-0/+11
* biology/chemeq: fix build on GCC (taken from dports)John Marino2016-12-181-0/+11
* Remove libintl.so.9 compatibility link that was added in r374303 toTijl Coosemans2016-12-093-2/+3
* Remove libjpeg.so.11 compatibility link that was added in r374303 toTijl Coosemans2016-12-091-0/+1
* Bump PORTREVISIONS for ports depending on the canonical version of GCC andGerald Pfeifer2016-12-077-5/+7
* biology/molden: distfile was updated in xwin.cKurt Jaeger2016-12-042-4/+4
* Do not use post-stage. Use post-install instead.Mathieu Arnold2016-12-021-1/+1
* biology/njplot: Add site in MASTER_SITES because package builders areJoseph Mingrone2016-11-281-2/+4
* biology/diamond: Update to version 0.8.28Joseph Mingrone2016-11-282-5/+6
* Fixup USE_GITHUB usage.Mathieu Arnold2016-11-262-3/+3
* Replace USE_GCC=4.9+ by USE_GCC=yes, now that lang/gcc and the defaultGerald Pfeifer2016-11-261-1/+1
* devel/boost-*: update to 1.62.0Jan Beich2016-11-231-0/+1
* - Remove unnecessary USES=shebangfixSunpoet Po-Chuan Hsieh2016-11-211-4/+8
* Bump PORTREVISIONS for ports depending on the canonical version of GCC andGerald Pfeifer2016-11-205-2/+5
* biology/avida: Fix ncurses from ports supportJohn Marino2016-11-191-1/+3
* biology/njplot: Revive and update to version 2.4Joseph Mingrone2016-11-165-0/+109
* Mark various leaf ports broken on aarch64, and, where appropriate, otherMark Linimon2016-11-114-2/+8
* Attempt to fix build on non-x86 archs.Mark Linimon2016-11-111-3/+5
* biology/seqtools: update 4.43.0 -> 4.44.1Kurt Jaeger2016-11-113-4/+14
* biology/molden: add missing LICENSE_NAMEKurt Jaeger2016-11-101-1/+2
* biology/molden: fix distinfo, set LICENSEKurt Jaeger2016-11-102-7/+11
* The 64-bit arm arch is actually spelled 'aarch64', not 'arm64'.Mark Linimon2016-11-093-3/+3
* Mark as broken on arm64.Mark Linimon2016-11-081-0/+2
* Mark broken on all tier-2 archs.Mark Linimon2016-11-081-0/+3
* Mark broken on the rest of the tier-2 archs: invokes x86 asm.Mark Linimon2016-11-081-1/+4
* biology/diamond: Update to version 0.8.26Joseph Mingrone2016-11-062-4/+4
* Cleanup no longer needed CHMOD usage after r424898.Mathieu Arnold2016-11-034-12/+5
* - Mark it BROKENWen Heping2016-10-281-1/+3
* Use USES=pathfix where applicable.Mathieu Arnold2016-10-214-21/+11
* ${RM} already has -f.Mathieu Arnold2016-10-213-3/+3
* biology/diamond: update to version 0.8.24Joseph Mingrone2016-10-172-4/+4
* biology/diamond: update to version 0.8.23Joseph Mingrone2016-10-102-4/+4
* Mark BROKEN: unfetchable, size mismatchAntoine Brodin2016-10-011-0/+1
* biology/blat: Fix build with non-base SSLJohn Marino2016-10-011-4/+4
* Update PORTREVISION and dinstinfo due to upstream tarball changeJoseph Mingrone2016-09-302-3/+4
* biology/paml: update to version 4.9c and various improvementsJoseph Mingrone2016-09-284-33/+48
* Update email address to jrm@FreeBSD.org for ports that I maintainJoseph Mingrone2016-09-243-5/+3
* - Update to 1.68Wen Heping2016-09-232-3/+4
* - Update biology/seqan and bilogy/seqan-apps to version 2.2.0 [1]Pawel Pekala2016-09-156-28/+39
* GOOGLE_CODE has gone away.Mathieu Arnold2016-09-141-0/+2
* - Update to 0.8.22Dmitry Marakasov2016-09-142-4/+4
* biology/ncbi-blast+: Remove redundant LIB_DEPENDS (bz2 libary)John Marino2016-09-111-3/+2
* - Update to 1.72Wen Heping2016-09-112-4/+4
* Most commonly used build systems support silent builds, when theyDmitry Marakasov2016-09-101-1/+1
* - Make configure script handle --disable-silent-rules gracefullyDmitry Marakasov2016-09-061-1/+1
* - Update to 0.8.20Wen Heping2016-09-062-4/+4
* - Replace Mk/bsd.linux-apps.mk and Mk/bsd.linux-rpm.mk withTijl Coosemans2016-09-062-4/+3
* biology/molden: 5.4 -> 5.7Kurt Jaeger2016-08-262-6/+4
* Update to version 0.8.19Pawel Pekala2016-08-262-4/+4
* - Mark BROKEN: does not fetch (distfile was removed from ftp)Dmitry Marakasov2016-08-221-0/+2
* biology/bedtools is not jobs safeJohn Marino2016-08-221-0/+2
* - Switch to options helpersDmitry Marakasov2016-08-183-16/+11
* Update biology/diamond to 0.8.18.Brad Davis2016-08-152-4/+4
* - Update to 1.9 [1]Wen Heping2016-08-082-10/+8
* Update to version 0.8.17Pawel Pekala2016-08-062-5/+5
* biology/seqtools: 4.42.1 -> 4.43.0Kurt Jaeger2016-07-313-17/+227
* Update to upstream release 0.8.16Thomas Zander2016-07-252-4/+4
* Cleanup $() variables in ports Makefiles.Mathieu Arnold2016-07-201-1/+1
* - update libgd to 2.2.2Dirk Meyer2016-07-201-1/+1
* When there is a do-install target, do not use a post-install target, doMathieu Arnold2016-07-193-4/+5
* Trim excess tabs, no-op changePawel Pekala2016-07-151-13/+13
* Update to version 0.8.14Pawel Pekala2016-07-152-4/+4
* - Update to 0.8.11Dmitry Marakasov2016-07-072-5/+5
* Remove expired ports without open PRs:Rene Ladan2016-07-057-161/+0
* - LICENSEDmitry Marakasov2016-07-022-10/+22
* biology/diamond: update 0.8.6 -> 0.8.9Jason Unovitch2016-06-302-4/+4
* - Add missing dependency, fixing buildDmitry Marakasov2016-06-241-1/+5
* - Switch to options helpersDmitry Marakasov2016-06-212-7/+11
* biology/diamond: update to 0.8.6Ruslan Makhmatkhanov2016-06-182-4/+4
* - 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
generated by cgit (git 2.34.1) at 2025-02-22 23:43:23 +0800