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* - Swap back from net/openmpi3 to net/openmpiDanilo Egea Gondolfo2020-04-211-3/+3
| | | | Notes: svn path=/head/; revision=532429
* - Swap back from net/openmpi3 to net/openmpiDanilo Egea Gondolfo2020-04-211-3/+3
| | | | Notes: svn path=/head/; revision=532428
* Update to 7.6.9Mateusz Piotrowski2020-04-192-4/+4
| | | | | | | | Release announcement: https://foldingforum.org/viewtopic.php?f=24&t=34466 Notes: svn path=/head/; revision=532099
* - Update net/openmpi to 4.0.3 (openmpi 1 is deprecated)Danilo Egea Gondolfo2020-04-191-3/+2
| | | | | | | | | - Remove option for net/openmpi2 from science/pnetcdf (net/openmpi2 is deprecated and will be removed) - Fix science/gromacs plist when MPI option is enabled - Bump PORTREVISION for all the consumers of net/openmpi Notes: svn path=/head/; revision=532095
* Update to 7.6.8Mateusz Piotrowski2020-04-182-6/+5
| | | | Notes: svn path=/head/; revision=532028
* - Move OpenMPI support to net/openmpi3. OpenMPI 1 and 2 were deprecated.Danilo Egea Gondolfo2020-04-151-2/+3
| | | | | | | Approved by: maintainer (e-mail) Notes: svn path=/head/; revision=531784
* biology/gcta: Genome-wide Complex Trait AnalysisJason W. Bacon2020-04-159-0/+218
| | | | | | | | | | | GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by genome- or chromosome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits. Notes: svn path=/head/; revision=531770
* Correct typo in pkg-message.Michael Gmelin2020-04-141-2/+2
| | | | | | | | | | Accidentally documented fahclient_donor as fahclient_user, which has a different meaning. PR: 245506 Notes: svn path=/head/; revision=531706
* Improve startup script, join "Team FreeBSD" by defaultMichael Gmelin2020-04-143-11/+85
| | | | | | | | PR: 245506 Approved by: 0mp (maintainer) Notes: svn path=/head/; revision=531701
* biology/py-macs2: Upgrade to 2.2.7.1Jason W. Bacon2020-04-143-5/+29
| | | | | | | | | Bug fix release Reported by: portscout Notes: svn path=/head/; revision=531674
* - Move OpenMPI support to net/openmpi3. OpenMPI 1 is deprecated.Danilo Egea Gondolfo2020-04-121-4/+4
| | | | Notes: svn path=/head/; revision=531485
* biology/fastp: Upgrade to 0.20.1Jason W. Bacon2020-04-093-8/+15
| | | | | | | | | Fix the plotly.js CDN issue Reported by: portscout Notes: svn path=/head/; revision=531215
* biology/star: Upgrade to 2.7.3aJason W. Bacon2020-04-092-4/+4
| | | | | | | Several compatibility and feature enhancements Notes: svn path=/head/; revision=531206
* Deprecate ports broken for more than 6 monthsAntoine Brodin2020-04-045-0/+10
| | | | Notes: svn path=/head/; revision=530719
* biology/ngs-sdk: Update 2.10.4 -> 2.10.5Yuri Victorovich2020-04-044-12/+12
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=530713
* Cosmetic changeSunpoet Po-Chuan Hsieh2020-04-021-2/+3
| | | | Notes: svn path=/head/; revision=530291
* Cosmetic changeSunpoet Po-Chuan Hsieh2020-04-021-2/+3
| | | | Notes: svn path=/head/; revision=530290
* kallisto: Patch for build with GCCJason W. Bacon2020-04-012-0/+11
| | | | | | | | PR: ports/245240 Submitted by: pkubaj Notes: svn path=/head/; revision=530250
* Update devel/tbb to 2020.2 and bump dependent port's revisionsGanael LAPLANCHE2020-04-011-0/+1
| | | | | | | Changelog: https://github.com/oneapi-src/oneTBB/blob/tbb_2020/CHANGES Notes: svn path=/head/; revision=530219
* Update WWWSunpoet Po-Chuan Hsieh2020-03-311-1/+1
| | | | Notes: svn path=/head/; revision=530167
* biology/cufflinks: Update 2.2.1-83 -> 2.2.1-89Yuri Victorovich2020-03-313-17/+10
| | | | | | | Add the pull request that fixes the boost::thread build failures. Notes: svn path=/head/; revision=529953
* Update WWWMateusz Piotrowski2020-03-302-2/+2
| | | | Notes: svn path=/head/; revision=529890
* biology/hyphy: Update to version 2.5.8Joseph Mingrone2020-03-283-5/+7
| | | | | | | Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.8 Notes: svn path=/head/; revision=529331
* Load appropriate Linuxulator bits automatically when starting serviceMateusz Piotrowski2020-03-232-1/+2
| | | | Notes: svn path=/head/; revision=528977
* Improve pkg-messageMateusz Piotrowski2020-03-221-6/+9
| | | | | | | | | | | - Fix some whitespace issues - Suggest the user to configure their user name and team ID. [1] - Link to a website where statistics are updated more often. Suggested by: netchild [1] Notes: svn path=/head/; revision=528927
* biology/seaview: Update version 5.0=>5.0.2Muhammad Moinur Rahman2020-03-222-4/+4
| | | | | | | Relnotes: http://doua.prabi.fr/software/seaview Notes: svn path=/head/; revision=528926
* Resurrect biology/linux-foldingathomeMateusz Piotrowski2020-03-217-0/+214
| | | | | | | | | | | Special thanks to netchild for inspiring bringing back this piece software to ports! Reviewed by: netchild, pi, salvadore Differential Revision: https://reviews.freebsd.org/D24127 Notes: svn path=/head/; revision=528886
* biology/diamond: Update to version 0.9.31.2Joseph Mingrone2020-03-212-4/+5
| | | | | | | | | Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.31 Also include two additional commits that fix a build error. Notes: svn path=/head/; revision=528881
* biology/canu: Upgrade to 2.0Jason W. Bacon2020-03-203-9/+4
| | | | | | | | | Several routine enhancements and bug fixes Reported by: portscout Notes: svn path=/head/; revision=528792
* biology/hyphy: Update to version 2.5.7Joseph Mingrone2020-03-202-4/+4
| | | | | | | Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.7 Notes: svn path=/head/; revision=528753
* Deprecate java/openjfx8-devel consumersTobias Kortkamp2020-03-191-0/+3
| | | | | | | | | | | Chase r527795 and put a deprecation notice on all openjfx8-devel dependent ports too. Also deprecate devel/gradle4 which is only needed to build igv and openjfx8-devel. Notes: svn path=/head/; revision=528706
* biology/hyphy: Update to version 2.5.6Joseph Mingrone2020-03-173-5/+4
| | | | | | | Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.6 Notes: svn path=/head/; revision=528590
* Mark BROKEN: fails to buildAntoine Brodin2020-03-101-0/+2
| | | | | | | | | | | ../include/pbcopper/json/internal/json.hpp:1229:9: error: static_assert failed due to requirement 'sizeof(nlohmann::basic_json<std::map, std::vector, std::__1::basic_string<char>, bool, long, unsigned long, double, std::allocator, adl_serializer>) == 0' "could not find from_json() method in T's namespace" static_assert(sizeof(BasicJsonType) == 0, ^ ~~~~~~~~~~~~~~~~~~~~~~~~~~ Reported by: pkg-fallout Notes: svn path=/head/; revision=528170
* Drop dependency on devel/openmpJan Beich2020-03-083-7/+5
| | | | | | | | | | - Drop if devel/llvm* was used as a substitute Approved by: yuri, rene (earlier version) Differential Revision: https://reviews.freebsd.org/D23020 Notes: svn path=/head/; revision=528082
* Deprecate some ports using deprecated version of pythonAntoine Brodin2020-03-082-0/+6
| | | | | | | With hat: portmgr Notes: svn path=/head/; revision=528058
* biology/ngs-sdk: Update 2.10.2 -> 2.10.4Yuri Victorovich2020-03-073-5/+5
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=527973
* 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
* Return theraven's ports to the pool after safekeeping his commit bit.Rene Ladan2020-03-051-1/+1
| | | | Notes: svn path=/head/; revision=527847
* biology/gatk: Update 4.1.4.1 -> 4.1.5.0Yuri Victorovich2020-03-043-18/+19
| | | | | | | Reported by: repology Notes: svn path=/head/; revision=527743
* biology/hyphy: Update to version 2.5.5Joseph Mingrone2020-03-023-15/+4
| | | | | | | Upstream changes: https://github.com/veg/hyphy/releases/tag/2.5.5 Notes: svn path=/head/; revision=527606
* biology/bowtie2: Upgrade to 2.4.1Jason W. Bacon2020-03-013-53/+30
| | | | | | | | | | Numerous bugfixes and enhancements Enable experimental support for aarch64 Reported by: portscout Notes: svn path=/head/; revision=527560
* biology/mrbayes: Update to version 3.2.7Joseph Mingrone2020-02-296-39/+60
| | | | | | | | PR: 243237 Submitted by: mzaki@e-mail.ne.jp (maintainer, with modifications) Notes: svn path=/head/; revision=527483
* Deprecate a few portsAntoine Brodin2020-02-233-0/+9
| | | | | | | With hat: portmgr Notes: svn path=/head/; revision=526925
* biology/stringtie: fix build on GCC architecturesPiotr Kubaj2020-02-231-1/+1
| | | | | | | | Use C++11 compiler: cc1plus: error: unrecognized command line option "-std=c++0x" Notes: svn path=/head/; revision=526916
* biology/hyphy: Update to version 2.5.4Joseph Mingrone2020-02-215-211/+45
| | | | | | | Upstream changes: https://github.com/veg/hyphy/releases Notes: svn path=/head/; revision=526622
* biology/vsearch: Upgrade to 2.14.2Jason W. Bacon2020-02-192-5/+5
| | | | | | | | | Numerous small bug fixes and enhancements Reported by: portscout Notes: svn path=/head/; revision=526534
* biology/stringtie: Update 1.3.4d -> 2.1.1Yuri Victorovich2020-02-165-97/+19
| | | | | | | | PR: 243718 Submitted by: Motomichi Matsuzaki <mzaki@e-mail.ne.jp> (maintainer) Notes: svn path=/head/; revision=526322
* biology/kallisto: Upgrade to 0.46.2Jason W. Bacon2020-02-152-6/+10
| | | | | | | | | | | Kallisto no longer builds in hdf5 by default, but it is still required for some downstream tools like Sleuth. Forcing it ON for now, but will disable it in a future upgrade. Reported by: portscout Notes: svn path=/head/; revision=526244
* biology/py-bx-python: Update 0.8.6 -> 0.8.8Yuri Victorovich2020-02-152-8/+8
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=526239
* biology/py-macs2: Bump revision for previous run dep additionJason W. Bacon2020-02-091-0/+1
| | | | Notes: svn path=/head/; revision=525659
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