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
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>
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>
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>
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
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>
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>
- Blixem can now accept a 'command' tag in a gff line for a region
feature. The given command should return gff and will be run by
blixem on the given region.
- Blixem now supports fetching sequence data over https.
genomics analysis tasks. The most widely-used of these tools enable genome
arithmetic, i.e., set theory on the genome. For example, with bedtools one
can intersect, merge, count, complement, and shuffle genomic intervals from
multiple files in common genomic formats such as BAM, BED, GFF/GTF, and VCF.
Although each individual utility is designed to do a relatively simple task,
e.g., intersect two interval files, more sophisticated analyses can be
conducted by stringing together multiple bedtools operations on the command
line or in shell scripts.
WWW: http://bedtools.readthedocs.org/
PR: 204536
Submitted by: scottcheloha@gmail.com
Changes:
- Missing hydrogens atoms of HETATM molecules (pdb files) are stored locally.
- Pdb files can now be clipped.
- Fixes missing residues. Introduces an alternative way of generating rotamers,
without using z-matrices. This potentially a faster algorithm.
- Supports Movie making through avconv/ffmpeg.
- calculates the Electron Localization Function (ELF).
- Updated code of ambfor/ambmd to speed up optimisations/MD of proteins
solvated in water (Jan, 2014).
PR: 204341
LICENSE= PD
Note that although Public Domain is not technically a license, it's
handled in the same way as licenses here, which is a common practice
(Arch, Gentoo, Fedora, Debian, even FOSSology do the same).
Convert all ports which redefine Public Domain LICENSE to LICENSE=PD.
Approved by: portmgr (bapt)
Differential Revision: D4149
This port will not build if ENOTRECOVERABLE is not defined, period.
It's not necessary to check OPSYS and version, just apply the fallback
definition if it's not defined. This unbreaks DragonFly after last
commit.
- Update ports to 1.3 and set BUILD_DEPENDS of dependent ports to require
version 1.3 of htslib.
- Add CURL option to htslib
- Add TEST_TARGET with perl and bash dependencies for testing
- Tidy up spacing and pkg-message's
PR: 205524
PR: 205525
PR: 205526
Submitted by: cartwright@asu.edu (maintainer)
2015-11-26 audio/pecl-id3: Broken for more than 6 months
2015-11-26 dns/geta: Broken for more than 6 months
2015-11-26 finance/openerp-web: Broken for more than 6 months
2015-11-26 devel/py-async: Further using of this module is not encouraged by upstream
2015-11-26 chinese/kon2: Depends on expiring chinese/cce
2015-11-26 games/linux-skulltag: Depends on expiring audio/linux-fmodapi
2015-11-26 archivers/wzip: Broken for more than 6 months
2015-11-26 databases/sybtcl: Broken for more than 6 months
2015-11-26 biology/povchem: Broken for more than 6 months
2015-11-26 audio/btc: Broken for more than 6 months
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2015-11-26 ftp/gnusget: Broken for more than 6 months
2015-11-26 comms/gpsk31: Broken for more than 6 months
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2015-11-26 cad/slffea: Broken for more than 6 months
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2015-11-26 cad/findhier: Broken for more than 6 months
2015-11-26 biology/njplot: Broken for more than 6 months
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2015-11-26 x11/avant-window-navigator: Broken for more than 6 months
2015-11-26 cad/geda-netlist: Broken for more than 6 months
2015-11-26 deskutils/libopensync-plugin-sunbird: Broken for more than 6 months
2015-11-26 biology/ortep3: Broken for more than 6 months
2015-11-26 astro/aa: Broken for more than 6 months
2015-11-26 french/belote: Broken for more than 6 months
2015-11-26 converters/p5-String-SetUTF8: Broken for more than 6 months
2015-11-26 cad/geda-examples: Broken for more than 6 months
2015-11-26 editors/yasnippet: Broken for more than 6 months
2015-11-26 audio/musica: Broken for more than 6 months
2015-11-26 graphics/rubyphoto: Broken for more than 6 months
2015-11-26 german/bsdpaste: Broken for more than 6 months
2015-11-26 audio/amrcoder: Broken for more than 6 months
2015-11-26 sysutils/bashburn: Broken for more than 6 months
2015-11-26 editors/e93: Broken for more than 6 months
2015-11-26 audio/tepsonic: Broken for more than 6 months
2015-11-26 astro/ephem: Broken for more than 6 months
2015-11-26 chinese/cce: Broken for more than 6 months
2015-11-26 graphics/qcread: Broken for more than 6 months
2015-11-26 databases/py-sqlkit: Broken for more than 6 months
2015-11-26 databases/usogres: Broken for more than 6 months
2015-11-26 cad/libgeda: Broken for more than 6 months
2015-11-26 chinese/p5-Lingua-ZH-BPMFConvert: Broken for more than 6 months
2015-11-26 french/alphabet_sounds_fr: Broken for more than 6 months
2015-11-26 deskutils/mrundlg: Broken for more than 6 months
2015-11-26 databases/erlang-mysql: Broken for more than 6 months
2015-11-26 graphics/linux-XnViewMP: Broken for more than 6 months
2015-11-26 deskutils/akamaru: Broken for more than 6 months
2015-11-26 dns/p5-Net-DNS-ZoneCheck: Broken for more than 6 months
2015-11-26 astro/dgpsip: Broken for more than 6 months
2015-11-26 databases/pecl-handlersocket: Broken for more than 6 months
2015-11-26 audio/cymbaline: Broken for more than 6 months
2015-11-26 french/dico: Broken for more than 6 months
2015-11-26 comms/qpage: Broken for more than 6 months
2015-11-26 audio/sonice: Broken for more than 6 months
2015-11-26 cad/geda-symbols: Broken for more than 6 months
2015-11-26 databases/java-mybatis: Broken for more than 6 months
2015-11-26 databases/openbase-jdbc: Broken for more than 6 months
2015-11-27 www/mediawiki119: Please upgrade to mediawiki-1.25
2015-11-28 www/R-cran-Rpad: Unmaintained upstream
Add working mirror.
Also update file size in distinfo - checksum is not changed
and I dunno why. But with old file size it warns that expected
size was different.
PR: 204491
Submitted by: Walter Schwarzenfeld <w.litter@aon.at>
- Blixem
o There is now an optional setting to highlight "maybe-canonical"
splice sites in Blixem. This can be used to help identify
problems where the strand is incorrect in the input data - it
highlights splice sites in a different colour if they would be
canonical were they on the other strand.
o Fixed a bug with colinearity lines when an alignment's cigar
string contains introns.
o There are now separate feedback boxes for the selected sequence
name coordinates. Hover over each box to see a tooltip describing
its contents.
