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2016-06-11- Fix run-time dependency issuesOlivier Duchateau
- Bump PORTREVISION PR: 209767 Submitted by: Joseph Mingrone (maintainer)
2016-06-10biology/seaview: Update version 4.5.4.8=>4.6Muhammad Moinur Rahman
- UNBREAK
2016-06-09Update to 0.8.5Matthew Seaman
PR: 209611 Submitted by: jrm@ftfl.ca (maintainer)
2016-06-08- Update to 1.35Wen Heping
2016-06-06Remove unneeded usage of:Mathieu Arnold
- MASTER_SITE_SUBDIR - ${MASTER_SITES_FOO} - :DEFAULT (and use a default when appropriate) Sponsored by: Absolight
2016-06-03Deprecate ports broken for more than 6 monthsAntoine Brodin
2016-05-27- Do install cmake and pkgconfig modulesDmitry Marakasov
- While here, switch to options helpers PR: 209710 Submitted by: h2+fbsdports@fsfe.org (maintainer)
2016-05-26biology/{htslib|samtools|bcftools}: 1.3 -> 1.3.1Kurt Jaeger
Changes: https://sourceforge.net/p/samtools/mailman/message/35033807/ PR: 209653 Submitted by: cartwright@asu.edu (maintainer)
2016-05-25Remove useless WRKSRC definitions.Mathieu Arnold
While there, correct DEV_WARNINGS when they occur. Sponsored by: Absolight
2016-05-19- Fix trailing whitespace in pkg-messagesDmitry Marakasov
Approved by: portmgr blanket
2016-05-19- Fix trailing whitespace in pkg-descrs, categories [a-f]*Dmitry Marakasov
Approved by: portmgr blanket
2016-05-18Fix DEPENDSAntoine Brodin
2016-05-16- Convert to USES=mysqlDmitry Marakasov
- Cosmetic fixes
2016-05-16- Update to 4.9aDmitry Marakasov
- While here, simplify WRKSRC and use options helpers PR: 209535 Submitted by: jrm@ftfl.ca (maintainer)
2016-05-13biology/bowtie2: 2.2.7 -> 2.2.8Kurt Jaeger
- Various website updates - Fixed the bowtie2-build issue that made TBB compilation fail PR: 208943 Submitted by: Joseph Mingrone <jrm@ftfl.ca> Approved by: Jason Bacon <bacon4000@gmail.com> (maintainer)
2016-05-13Prevent collision with getline(3)Baptiste Daroussin
2016-05-13Prevent collision with getline(3)Baptiste Daroussin
2016-05-11Prevent collision with getline(3)Baptiste Daroussin
While here regen patches
2016-05-10biology/seqan: update 1.3.1 -> 2.1.1Jason Unovitch
biology/seqan1: create port from current SeqAn 1.3.1 for legacy usage UPDATING: document SeqAn updates and seqan1 port for legacy usage PR: 204127 Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org>
2016-05-10New port: biology/seqan-appsJason Unovitch
SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. This port contains applications built on SeqAn and developed within the SeqAn project. Among them are famous read mappers like RazerS and Yara, as well as many other tools. Some applications are packaged seperately and the library can be found at biology/seqan. WWW: http://www.seqan.de/ PR: 204127 Submitted by: Hannes Hauswedell <h2+fbsdports@fsfe.org>
2016-05-09Add final slash in WWW entryOlivier Duchateau
2016-05-09The BIOM file format (canonically pronounced biome) is designed to be aOlivier Duchateau
general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project. The BIOM format is designed for general use in broad areas of comparative -omics. For example, in marker-gene surveys, the primary use of this format is to represent OTU tables: the observations in this case are OTUs and the matrix contains counts corresponding to the number of times each OTU is observed in each sample. With respect to metagenome data, this format would be used to represent metagenome tables: the observations in this case might correspond to SEED subsystems, and the matrix would contain counts corresponding to the number of times each subsystem is observed in each metagenome. Similarly, with respect to genome data, this format may be used to represent a set of genomes: the observations in this case again might correspond to SEED subsystems, and the counts would correspond to the number of times each subsystem is observed in each genome. WWW: http://biom-format.org/ PR: 209193 Submitted by: Joseph Mingrone
2016-05-07During the exp-run in bug 208158, it was found that biology/ugene givesDimitry Andric
errors with libc++ 3.8.0: In file included from src/QScoreAdapter.cpp:1: In file included from src/QScoreAdapter.h:4: In file included from ../../include/U2Core/MAlignment.h:1: In file included from ../../include/U2Core/../../corelibs/U2Core/src/datatype/MAlignment.h:25: In file included from ../../include/U2Core/../../corelibs/U2Core/src/datatype/MAlignmentInfo.h:25: In file included from /usr/local/include/qt5/QtCore/QString:1: In file included from /usr/local/include/qt5/QtCore/qstring.h:41: In file included from /usr/local/include/qt5/QtCore/qchar.h:37: In file included from /usr/local/include/qt5/QtCore/qglobal.h:39: /usr/include/c++/v1/cstddef:43:15: fatal error: 'stddef.h' file not found #include_next <stddef.h> ^ This is because the port tries to add /usr/include as a system include directory, using -isystem, and this screws up the order of include directories. Fix it by patching up a number of .pri files to avoid using the -isystem flag. Approved by: h2+fbsdports@fsfe.org (maintainer) PR: 209366 MFH: 2016Q2
2016-05-06DNA query sequences against a protein reference database (BLASTP and BLASTXWen Heping
alignment mode). The speedup over BLAST is up to 20,000 on short reads at a typical sensitivity of 90-99% relative to BLAST depending on the data and settings. WWW: http://ab.inf.uni-tuebingen.de/software/diamond/ PR: 208998 Submitted by: jrm@ftfl.ca
2016-05-01- Update to 1.14.8Danilo Egea Gondolfo
2016-04-22biology/seqtools: 4.41.1 -> 4.42.1Kurt Jaeger
- fixes build on 9.x - Added a feedback box to show the read depth at the selected coord. Hover over this box to see the specific base support (i.e. the number of A/C/G/Ts).
2016-04-21many ports: mark broken on powerpc64Steve Wills
2016-04-17- Switch to options helpersDmitry Marakasov
- Regenerate patches with `make makepatch` - Simplify plist
2016-04-17- Update to 1.66Wen Heping
PR: 208825 Submitted by: wen@ Approved by: maintainer
2016-04-16- Switch to options helpersDmitry Marakasov
2016-04-16Upgrade from 5.12.0 to 5.13.0. Release-announcement available here:Mikhail Teterin
https://groups.google.com/forum/#!topic/sbml-discuss/OEq_49c_X78 Notified by: portscout
2016-04-14Update to version 1.22.0, which now unfortunately requires Qt 5.x. AlsoAlexey Dokuchaev
since around v1.18.0, UGENE is using Google's Breakpad library for crash reporting, which is very system-specific and does not support FreeBSD at the moment. Due to lack of resources and interest in porting it, simply disable crash reporting code for the time being.
2016-04-10- Add LICENSEDmitry Marakasov
- Switch to options helpers
2016-04-01Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.Mathieu Arnold
With hat: portmgr Sponsored by: Absolight
2016-03-31- Update to 1.5.0Dmitry Marakasov
PR: 208351 Submitted by: wen@FreeBSD.org Approved by: mauricio@arareko.net (maintainer)
2016-03-29- Use more appropriate BROKEN instead of IGNOREDmitry Marakasov
PR: 208367 Submitted by: bacon4000@gmail.com (maintainer) Suggested by: rakuco
2016-03-27- Update to 5.12.0Wen Heping
2016-03-24- Clarify LICENSEDmitry Marakasov
- Add LICENSE_FILE - Remove USES=tar:bzip2 (incorrect and no-op with USE_GITHUB) - Drop unneeded (and incorrect anyway) PKG_CONFIG_PATH Approved by: portmgr blanket
2016-03-24Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.Dmitry Marakasov
A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the "compare-and-swap" CPU instruction to increase parallelism. WWW: http://www.genome.umd.edu/jellyfish.html PR: 207929 Submitted by: bacon4000@gmail.com
2016-03-23New port: biology/bowtie2.Raphael Kubo da Costa
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. This is Bowtie version 2, which will need to coexists with Bowtie 1 for the foreseeable future. Both are required by certain genomics pipelines, in some cases (e.g. Trinity) by the same pipeline. WWW: https://github.com/BenLangmead/bowtie2 PR: 207908 Submitted by: Jason Bacon <bacon4000@gmail.com>
2016-03-23New port: biology/slclust.Raphael Kubo da Costa
Slclust is a utility that performs single-linkage clustering with the option of applying a Jaccard similarity coefficient to break weakly bound clusters into distinct clusters. WWW: http://sourceforge.net/projects/slclust/ PR: 207997 Submitted by: Jason Bacon <bacon4000@gmail.com>
2016-03-17Trimmomatic performs a variety of useful trimming tasks for illuminaWen Heping
NGS paired-end and single ended data. WWW: http://www.usadellab.org/cms/?page=trimmomatic PR: 208044 Submitted by: bacon4000@gmail.com
2016-03-16New port: biology/p5-transdecoderKurt Jaeger
TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. WWW: http://transdecoder.github.io/ PR: 207993 Submitted by: Jason Bacon <bacon4000@gmail.com>
2016-03-14biology/seqtools: 4.40.0 -> 4.41.1Kurt Jaeger
- mostly internal changes, some build fixes
2016-03-08Always set the DEFAULT github DISTFILE with .tar.gz for EXTRACT_SUFX.Mathieu Arnold
Fix distinfo for the offending ports. lang/yorick's tag was moved, and the added patch was no longer needed. PR: 207644 Submitted by: mat Exp-run by by: antoine Sponsored by: Absolight Differential Revision: https://reviews.freebsd.org/D4268
2016-03-05New port: biology/bowtie.Raphael Kubo da Costa
Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. WWW: http://bowtie-bio.sourceforge.net/index.shtml PR: 206939 Submitted by: Jason Bacon <bacon4000@gmail.com>
2016-02-26New port: biology/vcftools.Raphael Kubo da Costa
A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project. WWW: https://github.com/vcftools/vcftools PR: 206926 Submitted by: Jason Bacon <bacon4000@gmail.com>
2016-02-26- Update to 3.2.0Wen Heping
- Update pkg-descr PR: 205890 Submitted by: tkato432@yahoo.com
2016-02-20- Update to 1.14.7Danilo Egea Gondolfo
2016-02-12- Update to 1.34Wen Heping
generated by cgit debian/1.2.3+git2.25.1-1-2-gaceb0 (git 2.25.1) at 2025-04-08 16:53:36 +0000