- 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
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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.
- Add License
- Add SIMD option disabled by default to avoid creating official
packags with CPU specific optimizations
- Add pkg-message explaining how to get an optimized binary
- Assign maintainership to submitter
PR: 203334
Submitted by: jwbacon at tds.net
Approved by: Maintainer timeout
genome (e.g. human genome). It has two major components, one for read shorter
than 150bp and the other for longer reads.
WWW: http://sourceforge.net/projects/bio-bwa/
PR: 203158
Submitted by: Jason Bacon <jwbacon@tds.net>
alignments of nucleotide or protein sequences. FastTree can handle alignments
with up to a million of sequences in a reasonable amount of time and memory.
WWW: http://www.microbesonline.org/fasttree/
PR: 203295
Submitted by: Jason Bacon <jwbacon@tds.net>
