summaryrefslogtreecommitdiff
path: root/biology (follow)
Commit message (Collapse)AuthorAgeFilesLines
* - Remove always-true/false conditions after FreeBSD 9, 10.1, 10.2 EOLDmitry Marakasov2017-01-092-15/+3
| | | | | | | Approved by: portmgr blanket Notes: svn path=/head/; revision=430947
* devel/boost-*: update to 1.63.0Jan Beich2017-01-061-1/+1
| | | | | | | | | | | Changes: http://www.boost.org/users/history/version_1_63_0.html PR: 215598 Exp-run by: antoine Approved by: office (bapt) MFH: 2017Q1 Notes: svn path=/head/; revision=430692
* Never set WRKSRC when using USE_GITHUB.Mathieu Arnold2017-01-032-4/+0
| | | | | | | | | | | | | If you want to set WRKSRC, set GH_PROJECT instead. - The GitHub URLs are case insensitive, but the distribution files you get out of them are not. - If the repository was renamed, the old URL will still work, but the distribution name will be ith the new name. Sponsored by: Absolight Notes: svn path=/head/; revision=430490
* Assume "pkg-config zlib" works after 9.x reached EOLJan Beich2017-01-031-3/+0
| | | | | | | | | | Many ports passed ZLIB_CFLAGS="-I/usr/include" ZLIB_LIBS="-L/usr/lib -lz" which is unsafe at least with lang/gcc* that override some system headers and have newer libgcc_s.so that our old version in base may not be forward-compatible with. Notes: svn path=/head/; revision=430483
* Remove BROKEN_FreeBSD_9Sunpoet Po-Chuan Hsieh2017-01-012-3/+0
| | | | | | | Approved by: portmgr (blanket) Notes: svn path=/head/; revision=430235
* biology/diamond: Update to version 0.8.30Joseph Mingrone2016-12-302-4/+4
| | | | | | | | | | | | | | Upstream changes: - slightly improved sensitivity - added option to report unaligned queries: --unal (0=no, 1=yes) - pairwise, XML and SAM format will report unaligned queries by default - added option to filter alignments by subject cover (--subject-cover) Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D9000 Notes: svn path=/head/; revision=429998
* biology/ncbi-blast+: Add MAKE_JOBS_UNSAFEJoseph Mingrone2016-12-221-0/+2
| | | | | | | | | PR: 214997 Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D8882 Notes: svn path=/head/; revision=429170
* - Update to 1.007001Sunpoet Po-Chuan Hsieh2016-12-202-4/+4
| | | | | | | Changes: http://search.cpan.org/dist/BioPerl-Run/Changes Notes: svn path=/head/; revision=429017
* biology/bowtie2: Update to version 2.2.9Joseph Mingrone2016-12-202-14/+18
| | | | | | | | | | | | - Update license information. - Add python to USES (bowtie2-build bowtie2-inspect need python) - Add DOCS and EXAMPLES options Approved by: AMDmi3 (mentor) swills (mentor) Differential Revision: https://reviews.freebsd.org/D8182 Notes: svn path=/head/; revision=429003
* biology/cd-hit: Update to bug-fix release 4.6.6Joseph Mingrone2016-12-202-5/+4
| | | | | | | | | | | | | | | | | Changes in version 4.6.6: Bug fix for cd-hit-dup in variable length input when write out R1 reads Changes in version 4.6.5: Add filter for -aL option so that short sequences will be skipped if not satisfy representative sequences' -aL requirement. This will make compute faster in clustering settings where sequences in the same cluster are required to have similar length using -aL -AL option (e.g. -aL 0.9). Approved by: AMDmi3 (mentor) swills (mentor) Differential Revision: https://reviews.freebsd.org/D8186 Notes: svn path=/head/; revision=429002
* biology/jellyfish: Update to version 2.2.6Joseph Mingrone2016-12-193-54/+56
| | | | | | | | | | | | | | Upstream changes since version 2.2.4: - Fix compilation warnings/errors with newer version of gcc (5.3 & 6.1). - Fix bug in parsing function that made it stop on sequences that consist of only empty lines. - New methods in bindings to enumerate the mers of a string. Approved by: AMDmi3 (mentor) Differential Revision: https://reviews.freebsd.org/D8204 Notes: svn path=/head/; revision=428954
* - Update *_DEPENDS: Bio::Coordinate family has been moved from ↵Sunpoet Po-Chuan Hsieh2016-12-191-2/+4
| | | | | | | | | biology/p5-BioPerl into biology/p5-Bio-Coordinate - Bump PORTREVISION for dependency change Notes: svn path=/head/; revision=428943
* - Add p5-Bio-Coordinate 1.007001Sunpoet Po-Chuan Hsieh2016-12-195-0/+58
| | | | | | | | | | Bio::Coordinate classes are used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples. WWW: http://search.cpan.org/dist/Bio-Coordinate/ Notes: svn path=/head/; revision=428942
* - Update to 1.007000Sunpoet Po-Chuan Hsieh2016-12-194-20/+29
| | | | | | | | | | | | | | | - Change MASTER_SITES back to CPAN - Update LICENSE - Add LICENSE_FILE - Use PORTDOCS - Convert to options target helper - Use INSTALL_SCRIPT - Pet portlint: fix diff header of patch file Changes: http://search.cpan.org/dist/BioPerl-Run/Changes Notes: svn path=/head/; revision=428941
* - Update to 1.007001Sunpoet Po-Chuan Hsieh2016-12-196-383/+180
| | | | | | | | | | | - Update *_DEPENDS - Use TEST_DEPENDS: Test::Most and URI::Escape are test-only dependencies - Use PORTDATA, PORTDOCS and PORTEXAMPLES Changes: http://search.cpan.org/dist/BioPerl/Changes Notes: svn path=/head/; revision=428940
* - Update to 2.5.0Wen Heping2016-12-195-68/+190
| | | | | | | | | PR: 214997 Submitted by: mzaki@e-mail.ne.jp Approved by: maintainer(timeout, > 14 days) Notes: svn path=/head/; revision=428903
* - Update to 2.40Sunpoet Po-Chuan Hsieh2016-12-183-10/+22
| | | | | | | | | | | - Update *_DEPENDS for biology/p5-bioperl renaming - Add NO_ARCH - Sort PLIST Changes: http://search.cpan.org/dist/Bio-Graphics/Changes Notes: svn path=/head/; revision=428874
* - Move biology/p5-bioperl-run to biology/p5-BioPerl-RunSunpoet Po-Chuan Hsieh2016-12-186-8/+10
| | | | | | | | | - Sort *_DEPENDS - Add NO_ARCH - Bump PORTREVISION for biology/p5-bioperl renaming Notes: svn path=/head/; revision=428872
* - Add LICENSE_FILESunpoet Po-Chuan Hsieh2016-12-181-2/+5
| | | | | | | | - Add NO_ARCH - Bump PORTREVISION for biology/p5-bioperl renaming Notes: svn path=/head/; revision=428871
* - Add LICENSESunpoet Po-Chuan Hsieh2016-12-181-4/+8
| | | | | | | | | - Add NO_ARCH - Sort *_DEPENDS - Bump PORTREVISION for biology/p5-bioperl renaming Notes: svn path=/head/; revision=428870
* - Add LICENSESunpoet Po-Chuan Hsieh2016-12-181-1/+7
| | | | | | | | - Add NO_ARCH - Bump PORTREVISION for biology/p5-bioperl renaming Notes: svn path=/head/; revision=428869
* - Move biology/p5-bioperl to biology/p5-BioPerlSunpoet Po-Chuan Hsieh2016-12-187-9/+7
| | | | | | | | - Sort *_DEPENDS - Bump PORTREVISION for dependent ports Notes: svn path=/head/; revision=428868
* biology/diamond: Update to version 0.8.29Joseph Mingrone2016-12-182-4/+4
| | | | | | | | | | | Upstream change: fixed an issue that could cause a crash when using view on incomplete DAA files Approved by: swills (mentor) Differential Revision: https://reviews.freebsd.org/D8832 Notes: svn path=/head/; revision=428850
* biology/protomol: Support build with C++11 (taken from dports)John Marino2016-12-185-0/+48
| | | | Notes: svn path=/head/; revision=428835
* biology/blat: Fix build on DF (taken from dports)John Marino2016-12-181-0/+14
| | | | Notes: svn path=/head/; revision=428834
* biology/lamarc: Fix build on DF (taken from dports)John Marino2016-12-181-0/+11
| | | | Notes: svn path=/head/; revision=428831
* biology/chemeq: fix build on GCC (taken from dports)John Marino2016-12-181-0/+11
| | | | Notes: svn path=/head/; revision=428829
* Remove libintl.so.9 compatibility link that was added in r374303 toTijl Coosemans2016-12-083-2/+3
| | | | | | | | prevent massive PORTREVISION bumps. Bump dependent ports that have not been bumped since. Notes: svn path=/head/; revision=428152
* Remove libjpeg.so.11 compatibility link that was added in r374303 toTijl Coosemans2016-12-081-0/+1
| | | | | | | | prevent massive PORTREVISION bumps. Bump dependent ports that have not been bumped since. Notes: svn path=/head/; revision=428135
* Bump PORTREVISIONS for ports depending on the canonical version of GCC andGerald Pfeifer2016-12-077-5/+7
| | | | | | | | | | | | | | | | | | lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some circumstances such as versions of FreeBSD or platforms), part II. The first part covered ports with USE_GCC=yes, USE_GCC=any, or one of gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang, c++11-lang, c++0x, c11 requested via USES=compiler. This adds ports with USES=fortran and ports using Mk/bsd.octave.mk which in turn has USES=fortran. PR: 214965 Reported by: thierry Notes: svn path=/head/; revision=428057
* biology/molden: distfile was updated in xwin.cKurt Jaeger2016-12-032-4/+4
| | | | Notes: svn path=/head/; revision=427627
* Do not use post-stage. Use post-install instead.Mathieu Arnold2016-12-021-1/+1
| | | | | | | | | | | | | | | The only reason to use post-stage is because the port needs to do "things" at a later time, like some plist manipulation. While there, fold post-install in do-install targets when they are defined. PR: 214780 Submitted by: mat Exp-run by: antoine Sponsored by: Absolight Notes: svn path=/head/; revision=427552
* biology/njplot: Add site in MASTER_SITES because package builders areJoseph Mingrone2016-11-281-2/+4
| | | | | | | | | | timing out during fetch. Approved by: AMDmi3 (mentor) Differential Revision: https://reviews.freebsd.org/D8651 Notes: svn path=/head/; revision=427329
* biology/diamond: Update to version 0.8.28Joseph Mingrone2016-11-282-5/+6
| | | | | | | | | | | | | | | Correct LICENSE and set LICENSE_FILE Upstream changelog: - support for gzip compressed files containing multiple gzip streams - support for the BLAST pairwise format (option -f 0) - slightly improved sensitivity Approved by: AMDmi3 (mentor) Differential Revision: https://reviews.freebsd.org/D8652 Notes: svn path=/head/; revision=427328
* Fixup USE_GITHUB usage.Mathieu Arnold2016-11-262-3/+3
| | | | | | | | | | It already sets DISTNAME to a very nice unique name, do not set it yourself. Sponsored by: Absolight Notes: svn path=/head/; revision=427136
* Replace USE_GCC=4.9+ by USE_GCC=yes, now that lang/gcc and the defaultGerald Pfeifer2016-11-251-1/+1
| | | | | | | version for GCC in the Ports Collection have moved to GCC 4.9. Notes: svn path=/head/; revision=427129
* devel/boost-*: update to 1.62.0Jan Beich2016-11-231-0/+1
| | | | | | | | | | | | | | | - Enable `long double` C99 math usage - Switch 9.x back to building with GCC Changes: http://www.boost.org/users/history/ PR: 199601 Submitted by: Chen Xu, bapt, amdmi3, truckman (based on) Reviewed by: rakuco (kde) (earlier version) Exp-run by: antoine (3 tries), truckman (consumers only, earlier versions) Approved by: bapt (office) Notes: svn path=/head/; revision=426908
* - Remove unnecessary USES=shebangfixSunpoet Po-Chuan Hsieh2016-11-201-4/+8
| | | | | | | - Convert to new options target helper Notes: svn path=/head/; revision=426677
* Bump PORTREVISIONS for ports depending on the canonical version of GCC andGerald Pfeifer2016-11-205-2/+5
| | | | | | | | | | | | lang/gcc which have moved from GCC 4.8.5 to GCC 4.9.4 (at least under some circumstances such as versions of FreeBSD or platforms). In particular that is ports with USE_GCC=yes, USE_GCC=any, or one of gcc-c++11-lib, openmp, nestedfct, c++11-lib as well as c++14-lang, c++11-lang, c++0x, c11 requested via USES=compiler. Notes: svn path=/head/; revision=426566
* biology/avida: Fix ncurses from ports supportJohn Marino2016-11-191-1/+3
| | | | Notes: svn path=/head/; revision=426378
* biology/njplot: Revive and update to version 2.4Joseph Mingrone2016-11-165-0/+109
| | | | | | | | Approved by: AMDmi3 (mentor) Differential Revision: https://reviews.freebsd.org/D8518 Notes: svn path=/head/; revision=426241
* Mark various leaf ports broken on aarch64, and, where appropriate, otherMark Linimon2016-11-114-2/+8
| | | | | | | | | tier-2 archs. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=425879
* Attempt to fix build on non-x86 archs.Mark Linimon2016-11-111-3/+5
| | | | | | | Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=425878
* biology/seqtools: update 4.43.0 -> 4.44.1Kurt Jaeger2016-11-113-4/+14
| | | | | | | | | - Blixem: Features can now be added to multiple different groups/filters. - Belvu: Fix a problem where column highlighting can get out of sync with the text. Notes: svn path=/head/; revision=425863
* biology/molden: add missing LICENSE_NAMEKurt Jaeger2016-11-101-1/+2
| | | | | | | Reported by: pkg-fallout Notes: svn path=/head/; revision=425830
* biology/molden: fix distinfo, set LICENSEKurt Jaeger2016-11-092-7/+11
| | | | | | | | | Submitted by: marino Reported by: Eduardo Lemos de Sa <eduardo.lemosdesa@gmail.com> MFH: 2016Q4 Notes: svn path=/head/; revision=425806
* The 64-bit arm arch is actually spelled 'aarch64', not 'arm64'.Mark Linimon2016-11-083-3/+3
| | | | Notes: svn path=/head/; revision=425758
* Mark as broken on arm64.Mark Linimon2016-11-081-0/+2
| | | | | | | Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=425689
* Mark broken on all tier-2 archs.Mark Linimon2016-11-081-0/+3
| | | | | | | Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=425675
* Mark broken on the rest of the tier-2 archs: invokes x86 asm.Mark Linimon2016-11-081-1/+4
| | | | Notes: svn path=/head/; revision=425664
generated by cgit v1.2.3 (git 2.25.1) at 2024-07-01 19:21:17 +0000