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* biology/py-crossmap: Update to 0.5.4Jason W. Bacon2021-04-212-5/+4
| | | | | Add viewchain command Reported by: portscout
* biology/py-crossmap: Fix build with Python 3.8+Kai Knoblich2021-04-211-1/+5
| | | | | | | | | | | | | | | | * Add missing dependency devel/py-nose that is required to build. With Python 3.6/3.7 there are no build issues because the sdist contains Python Eggs of "nose" for these versions. While I'm here: * Set NO_ARCH because the port has no architecture specific files. * Make it concurrent safe, package installs a script and bump PORTREVISION due package change. PR: 253815 Approved by: portmgr (build fix) MFH: No (The port was added after the 2021Q1 branch)
* biology/py-bigwig: Fix packaging with Python 3.8+Kai Knoblich2021-04-211-1/+1
| | | | | | | | | | | * Apply the same fix as in 9cb5898561b302d952fec8e2fac66a945a2c4915 by stripping libraries by wildcard paths. * Also use PYTHONPREFIX_SITELIBDIR instead PYTHON_SITELIBDIR to make the port PREFIX safe while I'm here. PR: 253815 Approved by: python (with hat)
* New port: biology/py-resdk: Resolwe SDK to interact with Resolwe server and ↵Yuri Victorovich2021-04-204-0/+38
| | | | Resolwe Bioinformatics
* biology/snpeff: Improvements to Makefile and patchesJason W. Bacon2021-04-194-12/+13
| | | | Reported by: Omp
* biology/abyss: Update 2.2.5 -> 2.3.0-3Yuri Victorovich2021-04-183-6/+11
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* biology/snpeff: Genetic variant annotation and effect prediction toolboxJason W. Bacon2021-04-187-0/+180
| | | | | | Genetic variant annotation and functional effect prediction toolbox. It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).
* biology/bbmap: BBMap short read aligner, and other bioinformatic toolsJason W. Bacon2021-04-186-0/+2064
| | | | | | | This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded.
* biology/bowtie2: Add support for powerpc64leJason W. Bacon2021-04-183-4/+17
| | | | | PR: 255092 Submitted by: pkubaj
* biology/readseq: Remove $FreeBSD$ tag inserted to silence portlintJason W. Bacon2021-04-181-2/+0
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* biology/readseq: Read and reformat biosequences, Java command-line versionJason W. Bacon2021-04-185-0/+38
| | | | | | Sequence reading library developed by the Ribosomal Database Project. It can handle genbank, embl, fasta, fastq, sff and sto files, can read from files or streams, and can handle indexing files.
* biology/seqkit: Change WWW to the project URL (from GitHub URL)Yuri Victorovich2021-04-171-1/+1
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* New port: biology/seqkit: Cross-platform and ultrafast toolkit for FASTA/Q ↵Yuri Victorovich2021-04-164-0/+42
| | | | file manipulation
* biology/ngs-sdk: Fix build on non-amd64 architectures that was broken by ↵Yuri Victorovich2021-04-151-1/+1
| | | | | | explicit 'amd64' instead of $ARCH Reported by: fallout
* Clean up some thingsTobias Kortkamp2021-04-151-1/+0
| | | | | | | | | - Remove duplicate variables - Remove nop variables - Sort categories - Remove redundant option descriptions that match the default ones Reported by: portscan
* devel/onetbb: Update to 2021.2.0 and bump dependenciesGanael LAPLANCHE2021-04-141-1/+1
| | | | Changelog: https://software.intel.com/content/www/us/en/develop/articles/intel-oneapi-threading-building-blocks-release-notes.html
* biology/diamond: Update to 2.0.9Joseph Mingrone2021-04-132-4/+4
| | | | https://github.com/bbuchfink/diamond/releases/tag/v2.0.9
* biology/mothur: Update to 1.45.2Jason W. Bacon2021-04-134-28/+25
| | | | | | Numerous bug fixes and enhancements since 1.43.0 Approved by: yuri
* biology/py-crossmap: Lift over genomics coordinates between assembliesJason W. Bacon2021-04-126-0/+59
| | | | | | | CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF, and gVCF.
* biology/py-bigwig: Python access to bigWig files using libBigWigJason W. Bacon2021-04-124-0/+30
| | | | | | A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files. This extension uses libBigWig for local and remote file access.
* biology/ncbi-vdb: Restore static libs installed with symlinks as shared libs ↵Yuri Victorovich2021-04-122-3/+18
| | | | | | | | are usually installed Symlinks like this libxx.a->libxx.a.N.N.N first looked broken but it turned out that this is intentional. PR: 223273
* biology/ngs-sdk: Restore static libs installed with symlinks as shared libs ↵Yuri Victorovich2021-04-122-3/+9
| | | | | | are usually installed Symlinks like this libxx.a->libxx.a.N.N.N first looked broken but it turned out that this is intentional.
* New port: biology/ncbi-vdb: NCBI's virtualized back-end for accessing ↵Yuri Victorovich2021-04-1231-0/+947
| | | | | | | Sequence Read Archive PR: 223273 Submitted by: Motomichi Matsuzaki <mzaki@niid.go.jp> (original version)
* biology/ngs-sdk: Improve the 'install' target and other parts of Makefile, ↵Yuri Victorovich2021-04-127-102/+62
| | | | report issues to upstream.
* biology/minimap2: Update to 2.18Jason W. Bacon2021-04-113-9/+7
| | | | | | Numerous bug fixes and a few minor improvements Reported by: portscout
* biology/vsearch: Update to 2.17.0Jason W. Bacon2021-04-102-4/+4
| | | | | | | Afterthoughts from the recent 2.16.0 release (Minor bug fixes and enhancements to the new orient subcommand) Reported by: portscout
* biology/hyphy: Update to 2.5.30Joseph Mingrone2021-04-082-4/+4
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* Remove expired ports:Rene Ladan2021-04-0717-380/+0
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | 2021-04-01 ftp/wzdftpd: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 astro/roadmap: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 games/cosmo: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 games/bomberinstinct: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 games/drm: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 games/bygfoot: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 games/cre: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 irc/hybserv: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 irc/xaric: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 mail/elmo: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 misc/cave: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 security/bugs: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 security/dmitry: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 security/doorman: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 shells/esh: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 sysutils/cpu: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 textproc/libcrm114: No known users, dead upstream 2021-04-01 x11/wmmatrix: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 x11/wmxss: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 x11/tycoon: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 x11/xgrab: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 x11/xbanner: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 x11/bricons: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 x11/xmon: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 games/cavezofphear: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 astro/saoimage: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 audio/ksmp3play: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 audio/jamin: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 audio/musicbox-tag-editor: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 audio/nspmod: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 audio/cdplay: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 audio/gimmix: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 audio/ghostess: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 audio/wmrecord: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 audio/toolame: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 audio/shout: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 biology/grappa: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 biology/phylip: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 biology/lagan: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 cad/varkon: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 cad/transcalc: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 comms/seyon: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 comms/efax: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 converters/vda2fbd: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 converters/shftool: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 devel/openzz: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 devel/sourcenav: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 devel/gb: Unmaintained and dead upstream 2021-04-01 dns/checkdns: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 dns/inadyn-mt: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 editors/gate: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 editors/thoteditor: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 emulators/cinc: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 emulators/e-uae: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 emulators/dtcyber: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 ftp/jftpgw: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-01 ftp/pureadmin: Unmaintained and dead upstream, does not build with -fno-common (llvm 11) 2021-04-02 textproc/hs-pandoc-citeproc: Integrated into textproc/hs-pandoc
* One more small cleanup, forgotten yesterday.Mathieu Arnold2021-04-07104-104/+0
| | | | Reported by: lwhsu
* all: Remove all other $FreeBSD keywords.Mathieu Arnold2021-04-063-7/+1
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* Remove # $FreeBSD$ from Makefiles.Mathieu Arnold2021-04-06187-188/+0
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* biology/pear-merger: enable on aarch64, armv6, armv7, riscv64Piotr Kubaj2021-04-061-5/+0
| | | | It should build now.
* biology/trimadap: fix build on powerpc64lePiotr Kubaj2021-04-061-1/+8
| | | | Requires GCC for its SSE translation.
* biology/pear-merger: fix build on non-x86Piotr Kubaj2021-04-061-0/+6
| | | | Builds fine with GCC.
* 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
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