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* devel/grpc: Update to 1.41.0Po-Chuan Hsieh2021-10-251-0/+1
| | | | | | - Changes: https://github.com/grpc/grpc/releases
* */Makefile: Sort SUBDIRsPo-Chuan Hsieh2021-10-251-1/+1
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* Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.)Alexey Dokuchaev2021-10-256-12/+12
| | | | | | | | | ONLY_FOR_ARCHS_REASON is used as part of the sentence and thus should start with lower-case letter and not end with a period which is added by the framework, similar to other knobs like BROKEN, IGNORE, et al. While here, remove needless quoting, add missing Oxford comma, expand contractions and jargonisms, use correct spelling for proper names.
* biology/py-resdk: Update 13.4.0 -> 13.6.0takefu2021-10-222-4/+4
| | | | PR: 259351
* biology/mafft: Update to 7.267Wen Heping2021-10-222-3/+4
| | | | | | PR: 259315 Reported by: gspurki@gmail.com Approved by: maintainer
* biology/bamutil: Update to 1.0.15Jason W. Bacon2021-10-202-6/+6
| | | | | | Numerous bug fixes and enhancements Changes: https://github.com/statgen/bamUtil/releases/tag/v1.0.15
* biology/fastp: Update to 0.23.1Jason W. Bacon2021-10-204-21/+56
| | | | | Performance improvements, more reproducible output Fix seg fault when running with no args
* *: fix tab vs. space issues, and comments according to the guide.Jimmy Olgeni2021-10-162-2/+2
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* biology/treekin: UnbreakYuri Victorovich2021-10-151-0/+22
| | | | | | Recent Lapack API changes broke it. PR: 259179
* biology/biostar-tools: Add py-deeptools to metaport depsJason W. Bacon2021-10-142-3/+4
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* biology/py-deeptools: User-friendly tools for exploring deep-sequencing dataJason W. Bacon2021-10-144-0/+39
| | | | | | | | | | deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.
* biology/ugene: update UniPro UGENE to version 40.1 (bugfix release).Alexey Dokuchaev2021-10-142-4/+4
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* biology/py-crossmap: chase ad5a0604c41cJan Beich2021-10-141-1/+1
| | | | | | make_index: biology/py-crossmap: no entry for biology/py-bigwig Reported by: indexbuild
* biology/py-bigwig: Rename to biology/py-pybigwigJason W. Bacon2021-10-134-1/+1
| | | | Fully match upstream name
* biology/py-pybigwig: remove, duplicate of biology/py-bigwigAntoine Brodin2021-10-135-42/+0
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* biology/py-deeptoolsintervals: Python interface for deepTools interval treesJason W. Bacon2021-10-134-0/+34
| | | | | Deeptools_intervals is an interval tree backend designed to interface with deepTools, supporting metadata associated with each interval.
* biology/py-py-pybigwig: Patch out setup.py warningJason W. Bacon2021-10-131-0/+11
| | | | Neglected to add this file during previous commit
* biology/py-pybigwig: Fix poudriere buildJason W. Bacon2021-10-132-1/+3
| | | | Typo in post-install
* biology/py-pybigwig: Python access to bigWig files using libBigWigJason W. Bacon2021-10-134-0/+30
| | | | | | py-bigwig is 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/py-py2bit: Python interface for 2bit packed nucleotide filesJason W. Bacon2021-10-134-0/+25
| | | | | | py2bit is a python extension, written in C, for quick access to 2bit files for randomly accessible, packed nucleotide sequences. The extension uses lib2bit for file access.
* biology/biostar-tools: Add biology/bamutil to metaport depsJason W. Bacon2021-10-122-3/+4
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* biology/bamutil: Utilities for working with SAM/BAM filesJason W. Bacon2021-10-127-0/+79
| | | | | | | Utilities for working on SAM/BAM files from The Center for Statistical Genetics at the University of Michigan School of Public Health. It includes numerous functions such as splitting, merging, trimming reads, filtering, validation, diff, etc.
* biology/diamond: Update to 2.0.12Joseph Mingrone2021-10-122-5/+4
| | | | https://github.com/bbuchfink/diamond/releases/tag/v2.0.12
* *: 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/py-biopython: Update to 1.79Wen Heping2021-10-122-4/+4
| | | | | | PR: 259046 Reported by: wen@ Approved by: maintainer
* biology/diamond: enable on powerpc64lePiotr Kubaj2021-10-091-1/+1
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* biology/diamond: enable on powerpc64Piotr Kubaj2021-10-081-1/+1
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* biology/libneurosim: New port: Common interfaces for neuronal simulatorsYuri Victorovich2021-10-085-0/+64
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* biology/hyphy: Enable on aarch64.Mikael Urankar2021-10-081-1/+1
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* biology/diamond: Enable on aarch64.Mikael Urankar2021-10-081-1/+1
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* biology/pooler: fix build on powerpcPiotr Kubaj2021-10-061-1/+6
| | | | | | | In file included from bit-common.c:63: In file included from ./bit-choice.h:23: In file included from ./triangle.h:44: ./openmp.h:19:10: fatal error: 'omp.h' file not found
* */*: Remove compiler:openmp from Mk/Uses/compiler.mkFernando Apesteguía2021-10-032-5/+4
| | | | | | | | | | | | | | | | | | The option implied a dependency on gcc but clang got openmp support long ago. Remove compiler:openmp from Mk/Uses/compiler.mk For ports using USE=compiler:openmp, just remove it and make them build with clang. Fix conditionals when necessary Bump PORTREVISION where appropriate If problem arises, they can be addressed by using USE_GCC=yes An update to the Porter's Handbook will follow. Approved by: portmgr (bapt) Differential Revision: https://reviews.freebsd.org/D31971
* biology/ncbi-cxx-toolkit: Update 25.0.0 -> 25.2.0Yuri Victorovich2021-10-012-8/+6
| | | | Reported by: upstream ML notification
* cleanup: drop support for EOL FreeBSD 11.XRene Ladan2021-09-305-10/+1
| | | | | | | | | | | | | | | | | Search criteria used: - 11.4 - OSREL* - OSVER* - *_FreeBSD_11 Input from: - adridg: devel/qca-legacy - jbeich: _WITH_DPRINTF, _WITH_GETLINE, GNU bfd workarounds - sunpoet: security/p5-*OpenSSL* Reviewed by: doceng, kde, multimedia, perl, python, ruby, rust Differential Revision: https://reviews.freebsd.org/D32008 Test Plan: make index
* biology/biostar-tools: Add biology/kallisto run depend to metaportJason W. Bacon2021-09-272-5/+6
| | | | Also clean up other deps for consistency
* biology/unikmer: Update 0.18.4 -> 0.18.8Yuri Victorovich2021-09-262-7/+7
| | | | Reported by: portscout
* biology/vcftools: Add CPE informationBernhard Froehlich2021-09-251-1/+3
| | | | Approved by: portmgr (blanket)
* biology/ucsc-userapps: Add "kent" command in ${PREFIX}/binJason W. Bacon2021-09-243-0/+63
| | | | | | | | | | | | Standard kent userapps commands are installed under ${PREFIX}/userapps because of multiple conflicts. The kent command turns the standard commands into subcommands, so no special PATH is needed. /usr/local/ucsc-userapps/bin/bigWigToBedGraph [args] can be run as kent bigWigToBedGraph [args]
* biology/emboss: Add "emboss" command in ${LOCALBASE}/binJason W. Bacon2021-09-244-2/+66
| | | | | | | | | | | | Standard emboss commands are installed under a special prefix because of multiple conflicts. The emboss command turns the standard commands into subcommands, so no special PATH is needed. /usr/local/emboss/bin/needle [args] can be run as emboss needle [args]
* biology/bioparser: Update 3.0.12-2 -> 3.0.15Yuri Victorovich2021-09-212-5/+4
| | | | Reported by: portscout
* */Makefile: Sort SUBDIRsPo-Chuan Hsieh2021-09-211-2/+2
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* biology/py-PySCeS: Update 0.9.8a -> 1.0.0Yuri Victorovich2021-09-202-9/+8
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* biology/py-libsedml: New port: SED-ML library for PythonYuri Victorovich2021-09-197-0/+89
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* biology/libsedml: New port: C++ SED-ML libraryYuri Victorovich2021-09-195-0/+149
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* biology/py-libnuml: Fix typoYuri Victorovich2021-09-191-1/+1
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* biology/py-libnuml: New port: Numerical Markup Language for PythonYuri Victorovich2021-09-196-0/+68
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* biology/libnuml: New port: C++ library for Numerical Markup LanguageYuri Victorovich2021-09-195-0/+80
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* biology/seqkit: Update 0.16.1 -> 2.0.1Yuri Victorovich2021-09-182-7/+7
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* 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/biolibc: Update to 0.2.0.11Jason W. Bacon2021-09-172-5/+5
| | | | | Regenerate man pages with improved auto-c2man Adds missing return value sections and improves formatting
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