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* biology/bioparser: Update 3.0.12 -> 3.0.12-2Yuri Victorovich2021-02-033-17/+17
| | | | | | | Install target is added. Notes: svn path=/head/; revision=563906
* biology/py-cutadapt: Update to 3.2Jason W. Bacon2021-02-024-12/+12
| | | | | | | | | | | | | biology/py-dnaio: Update to 0.5.0 archivers/py-xopen: Update to 1.0.0 Numerous bug fixes and enhancements since cutadapt 3.2 Document cutadapt dependency versions dnaio~=0.5.0 xopen~=1.0.0 Bump python dependency to 3.6+ to restrict package builds Notes: svn path=/head/; revision=563844
* biology/bowtie2: Reverse switch to devel/onetbbJason W. Bacon2021-01-301-2/+2
| | | | | | | | | Mistakenly believed onetbb was already committed PR: 252683 Notes: svn path=/head/; revision=563428
* biology/bowtie2: Switch to devel/onetbbJason W. Bacon2021-01-301-1/+2
| | | | | | | | PR: 252683 Submitted by: martymac Notes: svn path=/head/; revision=563427
* biology/vsearch: Update to 2.15.2Jason W. Bacon2021-01-303-10/+11
| | | | | | | | | Code clean up and modernization Reported by: portscout Notes: svn path=/head/; revision=563418
* Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+Sunpoet Po-Chuan Hsieh2021-01-305-5/+5
| | | | | | | PR: 250103 Notes: svn path=/head/; revision=563407
* biology/hyphy: Update to version 2.5.27Joseph Mingrone2021-01-272-4/+4
| | | | | | | https://github.com/veg/hyphy/releases/tag/2.5.27 Notes: svn path=/head/; revision=563045
* biology/kallisto: Add -lz for pending hdf5 upgradeJason W. Bacon2021-01-261-1/+2
| | | | | | | | PR: 252965 Submitted by: thierry Notes: svn path=/head/; revision=562627
* biology/bedtools: Upgrade to 2.30.0Jason W. Bacon2021-01-246-34/+46
| | | | | | | | | Several bug fixes and performance enhancements Reported by: portscout Notes: svn path=/head/; revision=562501
* biology/haplohseq: Fix example scripts for python 3Jason W. Bacon2021-01-236-43/+81
| | | | | | | Also clean up plist Notes: svn path=/head/; revision=562414
* biology/bedtools: License changed upstreamJason W. Bacon2021-01-221-1/+1
| | | | Notes: svn path=/head/; revision=562312
* biology/gatk: Add the WITH_LARGE_FILES option.Yuri Victorovich2021-01-221-0/+30
| | | | Notes: svn path=/head/; revision=562270
* biology/gatk: Update 4.1.8.1 -> 4.1.9.0Yuri Victorovich2021-01-212-6/+6
| | | | Notes: svn path=/head/; revision=562258
* Fix build on GCC-based systems by adding compiler:c++14-lang to USES:Mark Linimon2021-01-201-1/+1
| | | | | | | | | | | CMake Error in CMakeLists.txt: Target "runTests" requires the language dialect "CXX14" , but CMake does not know the compile flags to use to enable it. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=562108
* Add compiler:c++11-lang to USES to fix build on GCC-based systems:Mark Linimon2021-01-201-1/+1
| | | | | | | | | | | CMake Error in CMakeLists.txt: Target "rampler" requires the language dialect "CXX11" , but CMake does not know the compile flags to use to enable it. Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=562107
* biology/bioparser: Cosmetic changesYuri Victorovich2021-01-191-9/+9
| | | | Notes: svn path=/head/; revision=562040
* New port: biology/rampler: Standalone module for sampling genomic sequencesYuri Victorovich2021-01-195-0/+66
| | | | Notes: svn path=/head/; revision=562039
* New port: biology/edlib: Fast C++ library for sequence alignment using edit ↵Yuri Victorovich2021-01-195-0/+40
| | | | | | | distance Notes: svn path=/head/; revision=562038
* New port: biology/spoa: C++ implementation of the partial order alignment ↵Yuri Victorovich2021-01-196-0/+166
| | | | | | | (POA) algorithm Notes: svn path=/head/; revision=562036
* New port: biology/biosoup: Collection of C++ header-only data structures for ↵Yuri Victorovich2021-01-194-0/+46
| | | | | | | bioinformatics Notes: svn path=/head/; revision=562035
* New port: biology/bioparser: C++ header only parsing library for several ↵Yuri Victorovich2021-01-194-0/+49
| | | | | | | formats in bioinformatics Notes: svn path=/head/; revision=562033
* Mark BROKEN on riscv64 the same as on aarch64.Mark Linimon2021-01-191-2/+3
| | | | | | | | | | While here, pet portlint (Makevar order). Approved by: portmgr (tier-2 blanket) Obtained from: lonesome.com build testing Notes: svn path=/head/; revision=562006
* Mark BROKEN on riscv64 the same as armv*:Mark Linimon2021-01-191-0/+1
| | | | | | | | | | | | # make[2]: cannot open makefile.. Note the filname reported is "Makefile." (e.g. probably empty suffix). Approved by: portmgr (tier-2 blanket) Obtained from: lonesome.com build testing Notes: svn path=/head/; revision=562005
* biology/vsearch: enable on powerpc64lePiotr Kubaj2021-01-161-1/+1
| | | | Notes: svn path=/head/; revision=561748
* biology/hyphy: Update to version 2.5.26Joseph Mingrone2021-01-152-5/+4
| | | | | | | https://github.com/veg/hyphy/releases/tag/2.5.26 Notes: svn path=/head/; revision=561665
* biology/haplohseq: Restrict to python3Jason W. Bacon2021-01-152-2/+1
| | | | | | | | | Also remove extraneous @dir from plist Reported by: rene Notes: svn path=/head/; revision=561615
* Hook haplohseq to the buildAntoine Brodin2021-01-141-0/+1
| | | | Notes: svn path=/head/; revision=561604
* biology/haplohseq: Resurrect and fix python2 dependencyJason W. Bacon2021-01-1413-0/+308
| | | | | | | Move upstream to Github fork Notes: svn path=/head/; revision=561567
* Remove PY_SPHINX from ports using Python 3Danilo G. Baio2021-01-141-1/+1
| | | | | | | | Approved by: portmgr blanket Differential Revision: https://reviews.freebsd.org/D28093 Notes: svn path=/head/; revision=561562
* biology/iqtree: Remove USES=compiler:openmp, fix amd64 clang++ buildJoseph Mingrone2021-01-122-2/+14
| | | | | | | | | | | | | | - USES=compiler:openmp still forces building with GCC. This is no longer necessary on tier 1 platforms, which have openmp in base. - Mark broken on i386, because base clang doesn't have 64 bit atomic functions for i386 (see bug 230888). PR: 247753, 252379 Submitted by: cmt (based on) Notes: svn path=/head/; revision=561368
* biology/hyphy: Remove USES=compiler:openmpJoseph Mingrone2021-01-111-1/+2
| | | | | | | | | | USES=compiler:openmp still forces building with GCC. This is no longer necessary on tier 1 platforms, which have openmp in the base system. PR: 247753, 252379 Notes: svn path=/head/; revision=561239
* biology/star: Drop dependency on gccJason W. Bacon2021-01-112-15/+15
| | | | | | | | | Replace compiler:openmp with compiler:c++11-lang and localbase PR: port/247753, ports/252379 Notes: svn path=/head/; revision=561235
* biology/stacks: Drop dependency on gccJason W. Bacon2021-01-111-4/+4
| | | | | | | | | | Replace compiler:openmp with compiler:c++11-lang and localbase Set USE_GCC for i386 to work around limitations in clang atomic (PR 230888) PR: port/247753, ports/252379 Notes: svn path=/head/; revision=561234
* biology/ncbi-blast+: Drop dependency on gccJason W. Bacon2021-01-112-4/+26
| | | | | | | | | | | | Replace compiler:openmp with compiler:c++14-lang Clang build also requires localbase:ldflags and a source patch to explicitly set variables to shared GCC-based platforms still require -latomic PR: port/247753, ports/252379 Notes: svn path=/head/; revision=561233
* biology/gcta: Drop dependency on gccJason W. Bacon2021-01-111-10/+4
| | | | | | | | | | | Replace compiler:openmp with compiler:c++11-lang Clang build also requires localbase:ldflags Build tested on amd64, i386 and powerpc64 12.x-RELEASE PR: port/247753, ports/252379 Notes: svn path=/head/; revision=561231
* biology/fasttree: Drop dependency on gccJason W. Bacon2021-01-111-3/+1
| | | | | | | | | | Simply remove compiler:openmp Builds with base compiler on amd64, i386, and powerpc64 12.x-RELEASE PR: port/247753, ports/252379 Notes: svn path=/head/; revision=561229
* biology/cd-hit: Drop dependency on gccJason W. Bacon2021-01-111-2/+2
| | | | | | | | | | Simply remove compiler:openmp Builds with base compiler on amd64, i386, and powerpc64 PR: port/247753, ports/252379 Notes: svn path=/head/; revision=561228
* biology/canu: Drop dependency on gccJason W. Bacon2021-01-111-9/+3
| | | | | | | | | Replace compiler:openmp with compiler:c++11-lang and localbase PR: port/247753, ports/252379 Notes: svn path=/head/; revision=561227
* biology/py-biom-format: Update to version 2.1.10Joseph Mingrone2021-01-112-5/+4
| | | | | | | https://github.com/biocore/biom-format/releases/tag/2.1.10 Notes: svn path=/head/; revision=561187
* biology/hyphy: Update to version 2.5.25Joseph Mingrone2021-01-112-4/+4
| | | | | | | https://github.com/veg/hyphy/releases/tag/2.5.25 Notes: svn path=/head/; revision=561185
* biology/pooler: Upgrade to 1.76Jason W. Bacon2021-01-082-4/+4
| | | | | | | | | | Fixes race condition for make jobs in upstream Makefile PR: 252352 Submitted by: silas-freebsd@flatline.org.uk Notes: svn path=/head/; revision=560817
* biology/gemma: Upgrade to 0.98.3Jason W. Bacon2021-01-023-20/+4
| | | | | | | | | Minor bug fixes and enhancements Reported by: portscout Notes: svn path=/head/; revision=559975
* For ports on riscv64 that fail the same (or similar ways) to aarch64, markMark Linimon2021-01-026-0/+6
| | | | | | | | | | | them BROKEN. While here, pet portlint (Makevar order). Approved by: portmgr (tier-2 blanket) Notes: svn path=/head/; revision=559904
* - Update Unipro UGENE port to version 37.0Alexey Dokuchaev2020-12-3113-248/+56
| | | | | | | | | - Drop no longer used WebEngine dependencies - Force SSE2 on i386 (required for the build) - Chase HTTP 301 redirection in the WWW line Notes: svn path=/head/; revision=559737
* Drop python 2.7 support from a few portsAntoine Brodin2020-12-289-9/+9
| | | | | | | With hat: portmgr Notes: svn path=/head/; revision=559531
* Restrict to Java 8, since this doesn't compile with Java 11Greg Lewis2020-12-261-0/+1
| | | | | | | PR: 251774 Notes: svn path=/head/; revision=559318
* scipy 1.5.4 is only compatible with python 3.6+Antoine Brodin2020-12-242-2/+2
| | | | | | | Reported by: pkg-fallout Notes: svn path=/head/; revision=559053
* biology/hyphy: Update to version 2.5.24Joseph Mingrone2020-12-202-4/+4
| | | | | | | https://github.com/veg/hyphy/releases/tag/2.5.24 Notes: svn path=/head/; revision=558773
* biology/diamond: Update to version 2.0.6Joseph Mingrone2020-12-202-4/+4
| | | | | | | https://github.com/bbuchfink/diamond/releases/tag/v2.0.6 Notes: svn path=/head/; revision=558772
* Set CMAKE options explicitlySunpoet Po-Chuan Hsieh2020-12-201-0/+2
| | | | Notes: svn path=/head/; revision=558745
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