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* biology/subread: Update to 2.0.2Jason W. Bacon2021-03-304-19/+20
| | | | | | | | | Minor bug fixes and enhancements Reported by: portscout Notes: svn path=/head/; revision=569561
* biology/molden: Fix build with gfortran10Yuri Victorovich2021-03-291-1/+9
| | | | Notes: svn path=/head/; revision=569522
* biology/igv: Update 2.8.13 -> 2.9.4Yuri Victorovich2021-03-283-42/+44
| | | | Notes: svn path=/head/; revision=569400
* biology/vcflib: fix build on powerpc64lePiotr Kubaj2021-03-281-0/+7
| | | | | | | | | | | | Use GCC for its SSE -> AltiVec translation: In file included from src/ssw.cpp:38: In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13: In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13: /usr/lib/clang/11.0.1/include/mmintrin.h:33:5: error: use of undeclared identifier '__builtin_ia32_emms'; did you mean '__builtin_isless'? __builtin_ia32_emms(); Notes: svn path=/head/; revision=569399
* biology/vsearch: Update to 2.16.0Jason W. Bacon2021-03-242-4/+4
| | | | | | | | | | Add "orient" subcommand A few other fixes and enhancements Reported by: portscout Notes: svn path=/head/; revision=569151
* Mark ports recursively depending on Python 2.7 for expiration on June 23.Rene Ladan2021-03-242-0/+6
| | | | | | | | | | | | | | For ports optionally dependending on Python 2.7, just mark those options as expired. Remove konquerer from the x11/kde-baseapps metaport and bump its PORTREVISION. Submitted by: rene Reviewed by: portmgr, adridg, ehaupt, lme, madpilot, pizzamig, se, sunpoet, yuri Approved by: portmgr Differential Revision: https://reviews.freebsd.org/D28665 Notes: svn path=/head/; revision=569118
* biology/vcf2hap: Generate .hap file from VCF for haplohseqJason W. Bacon2021-03-234-0/+35
| | | | | | | | | vcf2hap is a simple tool for generating a .hap file from a VCF. The .hap file is required by haplohseq. vcf2hap is extremely fast and requires a trivial amount of memory regardless of the size of the VCF file. Notes: svn path=/head/; revision=569036
* biology/ad2vcf: Add allelic depth info from a SAM stream to a VCF fileJason W. Bacon2021-03-234-0/+36
| | | | | | | | | | ad2vdf extracts allelic depth info from a SAM stream and adds it to a corresponding single-sample VCF file. SAM input is read via stdin and the VCF input file is taken as a command-line argument. This allows expensive BAM/CRAM decoding to be performed in parallel by a separate samtools process. Notes: svn path=/head/; revision=569033
* - Update Unipro UGENE to version 38.0Alexey Dokuchaev2021-03-235-28/+8
| | | | | | | | | - Garbage-collect no longer needed patches - Make COMMENT shorter and closer to upstream - Stop building bundled SQLite, use ours! Notes: svn path=/head/; revision=569026
* Fix spelling mistakes, typos, poor wording, hyphenation, jargonisms,Alexey Dokuchaev2021-03-221-1/+1
| | | | | | | | contractions, "<portname> is ..." cases, missing Oxford commas, and other miscellaneous style bugs in the COMMENT line. Notes: svn path=/head/; revision=568947
* biology/vcf-split: Split a multi-sample VCF into single-sample VCFsJason W. Bacon2021-03-214-0/+35
| | | | | | | | | | | | Vcf-split splits a multi-sample VCF into single-sample VCFs, writing thousands of output files simultaneously. Parsing the TOPMed human chromosome 1 BCF with bcftools takes two days, so extracting the 137,977 samples one at a time or using thousands of parallel readers of the same file is impractical. Vcf-split solves this by generating thousands of single-sample outputs during a single sweep through the multi-sample input. Notes: svn path=/head/; revision=568922
* biology/biolibc: Low-level high-performance bioinformatics libraryJason W. Bacon2021-03-215-0/+33
| | | | | | | | | | | Biolibc is a library of fast, memory-efficient, low-level functions for processing biological data. Like libc, it consists of numerous disparate, general-purpose functions which could be used by a wide variety of applications. These include functions for streaming common file formats such as SAM and VCF, string functions specific to bioinformatics, etc. Notes: svn path=/head/; revision=568921
* biology/htslib: Update to 1.12Jason W. Bacon2021-03-2017-148/+32
| | | | | | | | | | | | | | biology/samtools: Update to 1.12 biology/bcftools: Update to 1.12 Numerous enhancements, performance improvements, and bug fixes since 1.11 Build-tested all other htslib dependents, no revbumps should be needed Reported by: portscout Notes: svn path=/head/; revision=568874
* biology/generand: Update to 0.1.2Jason W. Bacon2021-03-202-4/+4
| | | | | | | Generate proper VCF and SAM headers and valid CIGAR strings Notes: svn path=/head/; revision=568867
* biology/py-multiqc: Update to 1.10Jason W. Bacon2021-03-202-4/+5
| | | | | | | | | Numerous new features, a few bug fixes since 1.9 Reported by: portscout Notes: svn path=/head/; revision=568866
* biology/ngs-sdk: Update 2.10.9 -> 2.11.0Yuri Victorovich2021-03-203-5/+6
| | | | | | | Reported by: portscout Notes: svn path=/head/; revision=568842
* PyQt5: Update PyQt5 to 5.15.4 and py-qtbuilder to 1.9.1Loïc Bartoletti2021-03-161-1/+1
| | | | | | | | PR: 254218 Exp-run by: antoine Notes: svn path=/head/; revision=568547
* biology/generand: Generate random genomic data in FAST[AQ], SAM, or VCF formatJason W. Bacon2021-03-154-0/+27
| | | | | | | | | Generate random genomic data in FASTA/FASTQ, SAM, or VCF format, suitable for small academic examples or test inputs of arbitrary size. Output can be piped directly to programs or redirected to a file and edited to taste. Notes: svn path=/head/; revision=568501
* biology/abyss: Add PORTSCOUT lineYuri Victorovich2021-03-141-0/+2
| | | | Notes: svn path=/head/; revision=568329
* Move: biology/py-fastTSNE -> math/py-openTSNEYuri Victorovich2021-03-135-49/+0
| | | | | | | Project was renamed and reimplemented. Notes: svn path=/head/; revision=568296
* biology/gatk: Fix fetchYuri Victorovich2021-03-131-5/+5
| | | | | | | Reported by: fallout Notes: svn path=/head/; revision=568271
* biology/gatk: Update 4.1.9.0 -> 4.2.0.0Yuri Victorovich2021-03-122-7/+6
| | | | Notes: svn path=/head/; revision=568141
* biology/diamond: Update to 2.0.8Joseph Mingrone2021-03-112-4/+4
| | | | | | | https://github.com/bbuchfink/diamond/releases/tag/v2.0.8 Notes: svn path=/head/; revision=568088
* biology/hmmer: disable on powerpc64le and powerpcspePiotr Kubaj2021-03-101-1/+1
| | | | | | | | Altivec/VSX code in this port works only on big-endian POWER. powerpcspe has neither SSE2 nor Altivec. Notes: svn path=/head/; revision=568013
* biology/py-scikit-bio: fix build on powerpc64Piotr Kubaj2021-03-091-1/+1
| | | | | | | | | | | | | GCC is also necessary on powerpc64: In file included from skbio/alignment/_ssw_wrapper.c:626: In file included from skbio/alignment/_lib/ssw.h:17: In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13: In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13: /usr/lib/clang/11.0.1/include/mmintrin.h:50:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_vec_init_v2si(__i, 0); Notes: svn path=/head/; revision=567918
* biology/py-scikit-bio: fix build on powerpc64lePiotr Kubaj2021-03-091-2/+5
| | | | | | | | | | | | | Use GCC: In file included from skbio/alignment/_ssw_wrapper.c:626: In file included from skbio/alignment/_lib/ssw.h:17: In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13: In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13: /usr/lib/clang/11.0.1/include/mmintrin.h:50:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_vec_init_v2si(__i, 0); Notes: svn path=/head/; revision=567882
* PyQt5: Update PyQt5 to 5.15.3, QScintilla2 to 2.12.0, py-qtbuilder to 1.9.0Loïc Bartoletti2021-03-081-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | | * PyQt5: update to 5.15.3 This is a minor feature and bug-fix release. There are corresponding releases of the other PyQt5-related packages. - Added the missing QImage.setAlphaChannel(). - Support for the QtNetworkAuth library has been moved to a separate PyQtNetworkAuth package. - Wheels no longer bundle the corresponding Qt libraries and instead automatically install them from an external wheel. * QScintilla2: update to 2.12.0 This adds support for Qt6 and removes support for Qt4. - Change the new distname (again)i due to a conflict - Use the new sip-build system * devel/py-qtbuilder: update to 1.9.0 * devel/py-sip: fix flavor for sip-distinfo PR: 253865 Exp-run by: antoine Notes: svn path=/head/; revision=567825
* Unbreak INDEXAntoine Brodin2021-03-061-1/+1
| | | | Notes: svn path=/head/; revision=567519
* py-cutadapt: Update to 3.3Jason W. Bacon2021-03-062-5/+5
| | | | | | | | | | | | | Numerous small bug fixes and enhancements, code refactoring py-xopen: Update to 1.1.0 Required by cutadapt 3.3 Drop python 3.5 support Add isal support (not yet utilized in FreeBSD port) Notes: svn path=/head/; revision=567503
* biology/libbigwig: Update 0.4.4 -> 0.4.6Yuri Victorovich2021-03-063-7/+17
| | | | Notes: svn path=/head/; revision=567439
* biology/spoa: fix build on non-x86Piotr Kubaj2021-03-041-1/+7
| | | | | | | | | In file included from /wrkdirs/usr/ports/biology/spoa/work/spoa-4.0.7/src/dispatcher.cpp:7: /usr/local/include/cpuinfo_x86.h:228:2: error: "Including cpuinfo_x86.h from a non-x86 target." #error "Including cpuinfo_x86.h from a non-x86 target." Notes: svn path=/head/; revision=567333
* biology/bwa: fix build on powerpc64lePiotr Kubaj2021-03-021-2/+5
| | | | | | | | | | | | Use GCC's SSE->Altivec translation: In file included from ksw.c:29: In file included from /usr/lib/clang/11.0.1/include/emmintrin.h:13: In file included from /usr/lib/clang/11.0.1/include/xmmintrin.h:13: /usr/lib/clang/11.0.1/include/mmintrin.h:50:12: error: invalid conversion between vector type '__m64' (vector of 1 'long long' value) and integer type 'int' of different size return (__m64)__builtin_ia32_vec_init_v2si(__i, 0); Notes: svn path=/head/; revision=566960
* biology/py-bx-python: Update 0.8.9 -> 0.8.10Yuri Victorovich2021-02-272-9/+6
| | | | Notes: svn path=/head/; revision=566662
* biology/hyphy: Update to 2.5.29Joseph Mingrone2021-02-252-4/+4
| | | | | | | https://github.com/veg/hyphy/releases/tag/2.5.29 Notes: svn path=/head/; revision=566516
* biology/hyphy: Update to 2.5.28Joseph Mingrone2021-02-233-4/+5
| | | | | | | https://github.com/veg/hyphy/releases/tag/2.5.28 Notes: svn path=/head/; revision=566423
* Introduce devel/onetbb and mark devel/tbb as legacyGanael LAPLANCHE2021-02-191-2/+2
| | | | | | | | | | | | | | | | | | | | | | | | | | Intel oneAPI tbb 2021.1 (onetbb) has been released[1][2] and has deprecated several interfaces over tbb 2020, breaking most dependent ports. Old tbb 2020 will be kept for a certain time to allow transition but will be removed in a near future as it CONFLICTS with devel/onetbb. New ports should now use devel/onetbb instead of devel/tbb. We tried to move a maximum number of dependent ports to devel/onetbb (or disable dependency when not possible), but some of them still remain stuck to devel/tbb. Remaining ones have not been identified as major dependencies themselves and will be fixed as soon as updates are available from upstream. PR: 252648, 252688 [3], 252683 [4], 252651 [5], 252690 [3], 252693 [3], 252695 [3], 252696 [3], 252786 [3], 252649, 252868 [6], 252870 [5], 252684 [7], 252785 [7] Approved by: yuri [3], jwb [4], thierry [5], FreeBSD@Shaneware.biz [6], maintainer timeout [7] [1] https://software.intel.com/content/www/us/en/develop/articles/intel-oneapi-threading-building-blocks-release-notes.html [2] https://software.intel.com/content/www/us/en/develop/articles/tbb-revamp.html Notes: svn path=/head/; revision=566074
* biology/spoa: Fix build after recent devel/cereal update; Fix LIB_DEPENDSYuri Victorovich2021-02-192-4/+16
| | | | | | | Reported by: fallout Notes: svn path=/head/; revision=566037
* Mark BROKEN in 13/14 (via latest llvm update).Mark Linimon2021-02-171-0/+3
| | | | Notes: svn path=/head/; revision=565807
* biology/diamond: Update to 2.0.7Joseph Mingrone2021-02-172-4/+4
| | | | | | | https://github.com/bbuchfink/diamond/releases/tag/v2.0.7 Notes: svn path=/head/; revision=565520
* Update a few GNUstep ports:Neel Chauhan2021-02-141-1/+1
| | | | | | | | | | | | * devel/gnustep-make: Update to 2.8.0 * lang/gnustep-base: Update to 1.27.0 * x11-toolkits/gnustep-back: update to 0.28.0 * x11-toolkits/gnustep-gui: update to 0.28.0 Also bump PORTREVISION on dependent ports. Notes: svn path=/head/; revision=565273
* biology/py-multiqc: Update to 1.9Jason W. Bacon2021-02-052-6/+7
| | | | | | | | | Fix runtime error due to incompatibility of 1.8 with latest matplotlib Drop python2 support Numerous new features and bug fixes Notes: svn path=/head/; revision=564072
* biology/fastqc: Update to 0.11.9Jason W. Bacon2021-02-042-4/+4
| | | | | | | Minor bug fixes since 0.11.8 Notes: svn path=/head/; revision=564040
* 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
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