aboutsummaryrefslogtreecommitdiffstats
path: root/biology
Commit message (Expand)AuthorAgeFilesLines
* 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
* Convert a bunch of USE_BZIP2 to USES=tar:bzip2adamw2014-07-302-4/+2
* Rename biology/ patch-xy patches to reflect the files they modify.adamw2014-07-2811-13/+13
* - Update to 1.6.924 [1]wen2014-07-273-10/+11
* Really fix.mat2014-07-261-2/+0
* Fix build.mat2014-07-251-1/+1
* biology/p5-Bio-Graphics: 2.37 -> 2.38pi2014-07-242-3/+3
* Reset maintainership for ports not staged with no pending PRbapt2014-07-246-6/+6
* - Switch to USES=libtool, drop .la filesamdmi32014-07-232-3/+4
* biology/mummer: Use OPSYS with OSVERSIONmarino2014-07-201-1/+1
* biology/garlic: Stage properly to unbreakmarino2014-07-171-7/+5
* Add OPTIONS_DEFINE=DOCS for ports with %%PORTDOCS%% in the plist.adamw2014-07-161-0/+2
* Add DOCS to OPTIONS_DEFINE to ports that check for PORT_OPTIONS:MDOCS.adamw2014-07-152-14/+21
* biology/platon: Unbreak by hosting known distfiles elsewheremarino2014-07-132-6/+9
* biology/seqtools: 4.26 -> 4.27pi2014-07-132-4/+3
* Use gcc on all platforms.adamw2014-07-111-6/+1
* Stagify.vanilla2014-07-071-6/+5
* Missed a NOPORTDOCS.adamw2014-07-051-3/+4
* Remove NOPORTDOCS and NOPORTEXAMPLES from unstaged ports. Stage a couple whileadamw2014-07-051-21/+19
* - Chase database/sqlite3 slib bumpmiwi2014-06-281-0/+1
* Fix compilation on 10+ (clang)miwi2014-06-272-2/+10
* - Mark BROKENwen2014-06-261-0/+2
* Put HOME in MAKE_ARGS to handle pverride of HOME in MAKE_ENV from bsd.port.mkantoine2014-06-251-1/+2
* Use MAKE_CMD instead of GMAKEbapt2014-06-251-2/+2
* Mark as broken: no distinfo providedbapt2014-06-231-2/+1
* Mark as broken: no distinfo providedbapt2014-06-231-3/+1
* Fix shebang line in Perl and Python scripts.rakuco2014-06-201-13/+6
* Mark BROKEN: Fails to configureantoine2014-06-201-0/+2
* biology/blast: Deprecate for removal after 4 September 2014marino2014-06-191-0/+3
* Update to 1.2.10.rakuco2014-06-183-35/+23
* Update to 3.8.31.rakuco2014-06-185-89/+37
* Reset the 99 ports still listed under sylvio@marino2014-06-121-1/+1
* Remove all the bootstrap files (.bs) from the plists.mat2014-06-102-3/+0
* Remove indefinite articles and trailing periods from COMMENT, plusolgeni2014-06-096-6/+6
* Remove all space characters from Makefile assignments.olgeni2014-06-091-1/+1
* Stagify, remove BROKEN.vanilla2014-06-072-112/+107
* - Update to 6.6.0miwi2014-06-055-834/+1183
* Unbreakantoine2014-06-051-1/+1
* - Update to 4.5.2miwi2014-06-042-5/+5
* Update to 0.5.1 snapshot 20100824bapt2014-06-034-8/+49
* - add stage supportohauer2014-06-011-5/+1
* - add stage supportohauer2014-06-011-12/+6
* - add stage supportohauer2014-06-011-22/+16
* - add stage supportohauer2014-06-011-6/+3
* - add stage supportohauer2014-06-011-16/+4
* - add stage supportohauer2014-06-011-21/+8
* - I forgot to svn add a new patchdanilo2014-06-011-0/+10
* - Update from 1.13.5 to 1.13.7danilo2014-06-013-9/+9
* Add DOCS and EXAMPLE options to biology/mafftmilki2014-05-311-0/+2
* - Update to 1.6.923wen2014-05-305-1532/+1440
* biology/embassy: specify post-extraction with ${TAR}marino2014-05-291-1/+1
* Convert to USES=dos2unixbapt2014-05-261-2/+2
* Multiple ports: reset maintainerseadler2014-05-262-2/+2
* - Update to 4.5.1miwi2014-05-213-8/+13
* - Update to 7.149amdmi32014-05-213-32/+35
* Quote ${CC} and similar variables in MAKE_ARGS.tijl2014-05-211-1/+1
* - update to 1.31jadawin2014-05-162-3/+3
* - Update to 5.10.0wen2014-05-133-6/+39
* - Update to 5.9.0 [1]wen2014-05-133-40/+263
* Replace maintainer's email address with one that seems to workantoine2014-05-114-4/+4
* Catch a couple of missing convertsion to :tu/:tlbapt2014-05-051-1/+1
* Support stagebapt2014-05-051-20/+9
* Convert all :U to :tu and :L to :tlbapt2014-05-051-3/+3
* biology/seqtools: 4.25 -> 4.26, fix broken distinfo by upgradingpi2014-05-032-4/+5
* - Stage support [1]wen2014-05-023-1064/+5
* biology/seqtools: 4.24 -> 4.25pi2014-05-022-5/+4
* - Stageswills2014-04-272-1138/+2
* - Update to version 1.13.5miwi2014-04-264-43/+52
* - Un-break fetch stage: the name scheme of the source tarballs has changedriggs2014-04-235-12/+34
* Remove expired ports:rene2014-04-1812-635/+0
* The FreeBSD x11@ and graphics team proudly presentszeising2014-04-174-3/+4
* Remove expired ports:rene2014-04-1313-304/+0
* - Back to the heap, I don't use this port anymoreculot2014-04-121-1/+1
* Mark as broken unstaged perl portsbapt2014-04-092-0/+2
* Support stagebapt2014-04-072-32/+16
* - Update to 0.5.2wen2014-04-062-4/+5
* - Update to 2.3.6wen2014-04-062-4/+5
* - Update to 4.8wen2014-04-053-8/+8
* Unbreakantoine2014-03-281-1/+1
* - Fix PLISTsunpoet2014-03-262-0/+3
* - Update to 2.0sunpoet2014-03-262-3/+3
* Does not build with wx 3.0bapt2014-03-241-3/+3
* Add staging supportpawel2014-03-241-12/+5
* - Add staging supportpawel2014-03-241-19/+9
* - Add staging supportpawel2014-03-242-31/+31
* - Add staging supportpawel2014-03-241-17/+13
* Add staging supportpawel2014-03-242-34/+60
* - Add staging supportpawel2014-03-241-10/+8
* Add staging supportpawel2014-03-241-15/+8
* Add staging supportpawel2014-03-241-8/+5
* Deprecate: Broken for more than 6 monthsantoine2014-03-191-0/+2
* Support stagingehaupt2014-03-141-9/+3
* Support stagingehaupt2014-03-141-2/+2
* - Convert USE_GMAKE to USESmiwi2014-03-1310-11/+10
* Deprecate a few old unmaintained portsantoine2014-03-121-0/+2
* Update the default version of GCC used in the Ports Collection fromgerald2014-03-1112-10/+12
* biology/ssaha: undeprecate, this port fetches and builds fine.rene2014-03-091-3/+0
* Deprecate a few unmaintained ports (leaf ports, non staged and unmaintained s...antoine2014-03-092-0/+4
* Unbreakantoine2014-03-091-1/+0
* Convert b* to USES=zipbapt2014-03-075-10/+5
* Convert to dos2unixbapt2014-03-071-1/+1
* Update to version 1.13.1.danfe2014-03-073-4/+4
* biology/fasta3: Checked new distfile and regenerated distinfo to unbreakmarino2014-03-022-3/+8
* - Update to 35miwi2014-02-274-27/+50
* - Update to 5.0.7miwi2014-02-272-24/+21
* - Stage supportmiwi2014-02-272-21/+18
* - Repocopy print/py-reportlab to print/py-reportlab1tota2014-02-251-2/+2
* Remove trailing whitespaces from category biologyehaupt2014-02-2110-10/+10
* Convert all USE_FORTRAN=yes to "USES=fortran, USE_GCC=yes". In most casestijl2014-02-173-15/+13
* Support stagingehaupt2014-02-161-2/+1
* Support stagingehaupt2014-02-161-14/+7
* - Support stagingehaupt2014-02-161-9/+7
* Support stagingehaupt2014-02-161-8/+3
* Support stagingehaupt2014-02-161-10/+6
* Fix old makeplist bug.mat2014-02-122-1/+2
* According to the Porter's Handbook (5.12.2.3.) default options must be added toehaupt2014-02-1010-0/+20
* - Stage supportmiwi2014-02-102-22/+36
* Update WWWehaupt2014-02-091-1/+1
* Deprecate ports unmaintained for which distillator is not able to find public...bapt2014-02-081-0/+3
* biology/libgenome: Fix build on dragonflymarino2014-02-061-0/+10
* biology/tRNAscan-SE: Fix hardcoded perl pathmarino2014-02-061-0/+11
* biology/wise: Add dragonfly supportmarino2014-02-061-0/+13
* Drop maintainership on those.mat2014-02-061-1/+1
* Drop maintainership BOINC ports, old machine running them gave up.rene2014-02-051-1/+1
* - Stage supportmiwi2014-01-312-33/+31
* - Stage supportmiwi2014-01-311-1/+0
* - Stage supportmiwi2014-01-311-1/+0
* - Convert to PYDISTUTILS_AUTOPLISTmiwi2014-01-312-25/+3
* - Convert to PYDISTUTILS_AUTOPLISTmiwi2014-01-312-11/+3
* Unbreak the fetch: one of the documentation PDF files was rerolled.danfe2014-01-302-4/+2
* - Mark BROKEN because it does not fetchdecke2014-01-301-0/+2
* - fix pkg-plistaz2014-01-302-4/+3
* - Stagify; cleanup Makefile and reorder the knobs a bitdanfe2014-01-291-28/+21
* - Fix build on -currentmiwi2014-01-266-26/+60
* - Update to 1.9sunpoet2014-01-233-8/+7
* Fix properties on pkg-plistbapt2014-01-224-4/+0
* Support stagebapt2014-01-211-5/+4
* Support stagebapt2014-01-211-6/+5
* Support stagebapt2014-01-212-3/+1
* Support stagebapt2014-01-212-13/+26
* Stage supportantoine2014-01-181-15/+7
* - Update to version 1.13.0 and improve FreeBSD support; it also buildsdanfe2014-01-179-140/+378
* Reduce over inclusion of bsd.port.mkbapt2014-01-161-2/+1
* Reduce over inclusion of bsd.port.mkbapt2014-01-161-2/+1
* Reduce over inclusion of bsd.port.mkbapt2014-01-161-2/+1
* Reduce over inclusion of bsd.port.mkbapt2014-01-161-7/+3
* Reduce over inclusion of bsd.port.mkbapt2014-01-161-2/+1
* Support stagebapt2014-01-161-19/+10
* Python cleanup:rene2014-01-143-3/+3
* - Fix build with clangriggs2014-01-132-13/+8
* - add stage supportaz2014-01-062-6/+4
* - add stage supportaz2014-01-063-4/+2
* - support stageaz2014-01-056-135/+143
* Mark as broken: Invalid checksum, seems like the software was rerolledbapt2014-01-041-0/+2
* Convert biology to MDOCS and MEXAMPLESadamw2014-01-0314-20/+46
* - rename AL2 to APACHE20 in Mk/bsd.licenses.db.mkohauer2013-12-311-1/+1
* Stage supportantoine2013-12-311-3/+2
* Stage supportantoine2013-12-311-13/+4
* - USES=fortran gmake.tijl2013-12-292-16/+15
* The hmmer binary was renamed upstream to indicate that it is now anrene2013-12-292-6/+6
generated by cgit (git 2.34.1) at 2024-12-05 08:59:03 +0800