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* biology/jellyfish: Move man pages to share/manNuno Teixeira2024-03-022-2/+3
| | | | Approved by: portmgr (blanket)
* biology/jellyfish: Bump PORTREVISION for biology/htslib updateJason W. Bacon2023-01-061-1/+1
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* Remove WWW entries moved into port MakefilesStefan Eßer2022-09-071-2/+0
| | | | | | | | | | Commit b7f05445c00f has added WWW entries to port Makefiles based on WWW: lines in pkg-descr files. This commit removes the WWW: lines of moved-over URLs from these pkg-descr files. Approved by: portmgr (tcberner)
* Add WWW entries to port MakefilesStefan Eßer2022-09-071-0/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | It has been common practice to have one or more URLs at the end of the ports' pkg-descr files, one per line and prefixed with "WWW:". These URLs should point at a project website or other relevant resources. Access to these URLs required processing of the pkg-descr files, and they have often become stale over time. If more than one such URL was present in a pkg-descr file, only the first one was tarnsfered into the port INDEX, but for many ports only the last line did contain the port specific URL to further information. There have been several proposals to make a project URL available as a macro in the ports' Makefiles, over time. This commit implements such a proposal and moves one of the WWW: entries of each pkg-descr file into the respective port's Makefile. A heuristic attempts to identify the most relevant URL in case there is more than one WWW: entry in some pkg-descr file. URLs that are not moved into the Makefile are prefixed with "See also:" instead of "WWW:" in the pkg-descr files in order to preserve them. There are 1256 ports that had no WWW: entries in pkg-descr files. These ports will not be touched in this commit. The portlint port has been adjusted to expect a WWW entry in each port Makefile, and to flag any remaining "WWW:" lines in pkg-descr files as deprecated. Approved by: portmgr (tcberner)
* *: Clean up some thingsTobias Kortkamp2021-10-121-1/+1
| | | | | | | | | | | | - Fix typos - Fix overwritten variables with focus on master/slave ports - Remove unreferenced variables - Sort categories - Remove redundant option descriptions - Clean up commented PORTREVISION - Add missing USES Reported by: portscan
* biology/jellyfish: Switch to static tarball and update license infoJoseph Mingrone2021-09-172-10/+11
| | | | | | | | | | | | | The GitHub-generated tarballs require reautoconf and more dependencies including gettext, regardless whether the NLS knob is turned off. https://github.com/gmarcais/Jellyfish/issues/138#issuecomment-463272029 This update also fixes a build issue when the NLS knob was turned off. http://pkg.ftfl.ca/data/13amd64-default/2021-09-16_13h45m55s/logs/errors/Jellyfish-2.3.0_1.log Differential Revision: https://reviews.freebsd.org/D31984 Co-authored-by: Jason W. Bacon <jwb@FreeBSD.org>
* biology/jellyfish: Fix unused open mode variableJason W. Bacon2021-09-112-0/+12
| | | | | PR: 258397 Reported by: dim
* biology/jellyfish: Update to 2.3.0Jason W. Bacon2021-08-226-58/+4
| | | | Changelog: https://github.com/gmarcais/Jellyfish/releases/tag/v2.3.0
* One more small cleanup, forgotten yesterday.Mathieu Arnold2021-04-071-1/+0
| | | | Reported by: lwhsu
* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-061-1/+0
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* biology/htslib: Upgrade to 1.10.2Jason W. Bacon2020-08-031-1/+1
| | | | | | | | | | | | Numerous bug fixes and enhancements since 1.9: https://github.com/samtools/htslib/tags Bump PORTREVISION on dependents that don't require additional patching PR: 248089 Notes: svn path=/head/; revision=544090
* biology/jellyfish: Patch for clang 10Jason W. Bacon2020-03-073-3/+23
| | | | | | | | | | Add cast to silence implicit conversion error PR: ports/244645 Submitted by: dim Notes: svn path=/head/; revision=527971
* Drop C++11 workaround for GCC < 6 after r449590Jan Beich2019-09-142-36/+1
| | | | | | | | | | | lang/gcc5 will expire in ~1 month. If someone still uses lang/gcc48 they should backport C++11 fix instead. QA on GCC architecuters is currently limited to powerpc64 which uses GCC_DEFAULT. PR: 193528 Notes: svn path=/head/; revision=512079
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2019-07-261-1/+1
| | | | | | | | | | | | | | | | | | as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3 to GCC 9.1 under most circumstances now after revision 507371. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang, c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib plus, everything INDEX-11 shows with a dependency on lang/gcc9 now. PR: 238330 Notes: svn path=/head/; revision=507372
* biology/jellyfish: Upgrade to 2.2.10, patch for powerpc64Jason W. Bacon2019-05-138-16/+79
| | | | | | | | PR: 237868 Submitted by: pkubaj Notes: svn path=/head/; revision=501578
* These ports now build on aarch64.Mark Linimon2019-05-031-3/+1
| | | | | | | | | | Where necessary, pet portlint. Approved by: portmgr Obtained from: aarch64 TRYBROKEN run Notes: svn path=/head/; revision=500752
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2018-12-121-1/+1
| | | | | | | | | | | | | | | | | | defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t GCC 8.2 under most circumstances. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang, c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib plus, as a double check, everything INDEX-11 showed depending on lang/gcc7. PR: 231590 Notes: svn path=/head/; revision=487272
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2018-07-291-1/+1
| | | | | | | | | | | | | | | | | in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which has now moved from GCC 6 to GCC 7 by default. This includes ports - featuring USE_GCC=yes or USE_GCC=any, - featuring USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and those - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x, c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib. PR: 222542 Notes: svn path=/head/; revision=475857
* Multiple ports:Jason W. Bacon2018-01-311-2/+1
| | | | | | | | | | | Change maintainer email bacon4000@gmail.com to jwb@FreeBSD.org Remove Created by comments for same user Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14128 Notes: svn path=/head/; revision=460452
* Bump PORTREVISION for ports depending on the canonical version of GCCGerald Pfeifer2017-09-101-1/+1
| | | | | | | | | | | | | | | | | (via Mk/bsd.default-versions.mk and lang/gcc) which has moved from GCC 5.4 to GCC 6.4 under most circumstances. This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using Mk/bsd.octave.mk which in turn features USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++11-lang, c++14-lang, c++0x, c11, or gcc-c++11-lib. PR: 219275 Notes: svn path=/head/; revision=449591
* Bump PORTREVISIONs for ports depending on the canonical version of GCC andGerald Pfeifer2017-04-011-0/+1
| | | | | | | | | | | | | | | | | lang/gcc which have moved from GCC 4.9.4 to GCC 5.4 (at least under some circumstances such as versions of FreeBSD or platforms). This includes ports - with USE_GCC=yes or USE_GCC=any, - with USES=fortran, - using using Mk/bsd.octave.mk which in turn has USES=fortran, and - with USES=compiler specifying openmp, nestedfct, c++11-lib, c++14-lang, c++11-lang, c++0x, c11, or gcc-c++11-lib. PR: 216707 Notes: svn path=/head/; revision=437439
* Remove BROKEN_FreeBSD_9Sunpoet Po-Chuan Hsieh2017-01-011-1/+0
| | | | | | | Approved by: portmgr (blanket) Notes: svn path=/head/; revision=430235
* 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
* Mark various leaf ports broken on aarch64, and, where appropriate, otherMark Linimon2016-11-111-0/+1
| | | | | | | | | tier-2 archs. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=425879
* Use USES=pathfix where applicable.Mathieu Arnold2016-10-211-7/+1
| | | | | | | | | | | PR: 213195 Submitted by: mat Exp-run by: antoine Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D8093 Notes: svn path=/head/; revision=424427
* Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.Mathieu Arnold2016-04-011-1/+1
| | | | | | | | With hat: portmgr Sponsored by: Absolight Notes: svn path=/head/; revision=412344
* - Use more appropriate BROKEN instead of IGNOREDmitry Marakasov2016-03-291-4/+2
| | | | | | | | | PR: 208367 Submitted by: bacon4000@gmail.com (maintainer) Suggested by: rakuco Notes: svn path=/head/; revision=412137
* Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.Dmitry Marakasov2016-03-245-0/+145
A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. WWW: http://www.genome.umd.edu/jellyfish.html PR: 207929 Submitted by: bacon4000@gmail.com Notes: svn path=/head/; revision=411785
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