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freebsd-ports/biology
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Joseph Mingrone ac30d1f025 biology/diamond: Update to version 0.8.31. 
Upstream changelog:

  - Added compositional score adjustments (option --comp-based-stats
    (0,1)). This is a useful feature for filtering false positive hits and
    is enabled by default.

  - Removed --single-domain option and replaced by --max-hsps, to set the
    maximum number of Hsps per query/subject pair, to be consistent with
    BLAST. This option is set to 1 by default as getting more than 1 Hsp
    per subject seems to be confusing users.

  - Added option --no-self-hits to filter identical self-hits.

Approved by:	AMDmi3 (mentor)
Differential Revision:	https://reviews.freebsd.org/D9134
2017-01-12 23:23:19 +00:00
..
ariadne
artemis
avida biology/avida: Fix ncurses from ports support 2016-11-19 14:56:46 +00:00
babel
bcftools
bedtools
biococoa
biojava - Mark it BROKEN 2016-10-28 01:49:40 +00:00
blat biology/blat: Fix build on DF (taken from dports) 2016-12-18 04:46:53 +00:00
bowtie Bump PORTREVISIONS for ports depending on the canonical version of GCC and 2016-11-20 09:38:08 +00:00
bowtie2 biology/bowtie2: Update to version 2.2.9 2016-12-20 17:01:27 +00:00
bwa Attempt to fix build on non-x86 archs. 2016-11-11 09:07:21 +00:00
cd-hit biology/cd-hit: Update to bug-fix release 4.6.6 2016-12-20 16:48:12 +00:00
cdbfasta
chemeq biology/chemeq: fix build on GCC (taken from dports) 2016-12-18 04:22:26 +00:00
clustalw
consed
crux Bump PORTREVISIONS for ports depending on the canonical version of GCC and 2016-12-07 13:24:56 +00:00
diamond biology/diamond: Update to version 0.8.31. 2017-01-12 23:23:19 +00:00
emboss
fasta
fasta3
fastdnaml
fastool Never set WRKSRC when using USE_GITHUB. 2017-01-03 18:12:13 +00:00
fasttree Bump PORTREVISIONS for ports depending on the canonical version of GCC and 2016-11-20 09:38:08 +00:00
fastx-toolkit
fluctuate
garlic
gff2ps
gmap The 64-bit arm arch is actually spelled 'aarch64', not 'arm64'. 2016-11-08 19:29:56 +00:00
gperiodic Remove libintl.so.9 compatibility link that was added in r374303 to 2016-12-08 19:52:19 +00:00
grappa
hmmer
htslib Use USES=pathfix where applicable. 2016-10-21 15:21:13 +00:00
iolib
jalview
jellyfish Remove BROKEN_FreeBSD_9 2017-01-01 03:45:12 +00:00
lagan
lamarc biology/lamarc: Fix build on DF (taken from dports) 2016-12-18 04:34:33 +00:00
libgtextutils Use USES=pathfix where applicable. 2016-10-21 15:21:13 +00:00
libsbml Cleanup no longer needed CHMOD usage after r424898. 2016-11-02 22:45:14 +00:00
linux-foldingathome
mafft
mapm3
migrate
molden Bump PORTREVISIONS for ports depending on the canonical version of GCC and 2016-12-07 13:24:56 +00:00
mopac Bump PORTREVISIONS for ports depending on the canonical version of GCC and 2016-12-07 13:24:56 +00:00
mrbayes
mummer
muscle Mark various leaf ports broken on aarch64, and, where appropriate, other 2016-11-11 09:31:02 +00:00
ncbi-blast+ biology/ncbi-blast+: Add MAKE_JOBS_UNSAFE 2016-12-22 16:49:16 +00:00
ncbi-toolkit Remove libjpeg.so.11 compatibility link that was added in r374303 to 2016-12-08 16:39:11 +00:00
njplot biology/njplot: Add site in MASTER_SITES because package builders are 2016-11-28 15:19:42 +00:00
p5-AcePerl Mark various leaf ports broken on aarch64, and, where appropriate, other 2016-11-11 09:31:02 +00:00
p5-Bio-ASN1-EntrezGene - Add LICENSE 2016-12-18 15:25:13 +00:00
p5-Bio-Coordinate - Add p5-Bio-Coordinate 1.007001 2016-12-19 15:54:39 +00:00
p5-Bio-Das - Add LICENSE 2016-12-18 15:25:18 +00:00
p5-Bio-Das-Lite
p5-Bio-GFF3
p5-Bio-Glite
p5-Bio-Graphics - Update *_DEPENDS: Bio::Coordinate family has been moved from biology/p5-BioPerl into biology/p5-Bio-Coordinate 2016-12-19 15:54:43 +00:00
p5-Bio-MAGETAB
p5-Bio-NEXUS
p5-Bio-Phylo - Add LICENSE_FILE 2016-12-18 15:25:22 +00:00
p5-Bio-SCF
p5-BioPerl - Update to 1.007001 2016-12-19 15:54:29 +00:00
p5-BioPerl-Run - Update to 1.007001 2016-12-20 18:35:26 +00:00
p5-transdecoder Never set WRKSRC when using USE_GITHUB. 2017-01-03 18:12:13 +00:00
paml Cleanup no longer needed CHMOD usage after r424898. 2016-11-02 22:45:14 +00:00
phrap
phred
phylip
phyml
plink Bump PORTREVISIONS for ports depending on the canonical version of GCC and 2016-12-07 13:24:56 +00:00
plinkseq Mark various leaf ports broken on aarch64, and, where appropriate, other 2016-11-11 09:31:02 +00:00
primer3
protomol biology/protomol: Support build with C++11 (taken from dports) 2016-12-18 05:34:42 +00:00
psi88 Bump PORTREVISIONS for ports depending on the canonical version of GCC and 2016-12-07 13:24:56 +00:00
py-biom-format
py-biopython
pycogent
pyfasta
python-nexus
recombine
ruby-bio
samtools
seaview
seqan
seqan1
seqan-apps - Remove always-true/false conditions after FreeBSD 9, 10.1, 10.2 EOL 2017-01-09 13:16:49 +00:00
seqio
seqtools Remove BROKEN_FreeBSD_9 2017-01-01 03:45:12 +00:00
sim4
slclust
ssaha Bump PORTREVISIONS for ports depending on the canonical version of GCC and 2016-11-20 09:38:08 +00:00
t_coffee Bump PORTREVISIONS for ports depending on the canonical version of GCC and 2016-12-07 13:24:56 +00:00
tinker Bump PORTREVISIONS for ports depending on the canonical version of GCC and 2016-12-07 13:24:56 +00:00
treepuzzle
treeviewx
trimmomatic
tRNAscan-SE
ugene - Remove always-true/false conditions after FreeBSD 9, 10.1, 10.2 EOL 2017-01-09 13:16:49 +00:00
vcftools Assume "pkg-config zlib" works after 9.x reached EOL 2017-01-03 17:06:49 +00:00
velvet
wise Remove libintl.so.9 compatibility link that was added in r374303 to 2016-12-08 19:52:19 +00:00
xmolwt Remove libintl.so.9 compatibility link that was added in r374303 to 2016-12-08 19:52:19 +00:00
Makefile - Add p5-Bio-Coordinate 1.007001 2016-12-19 15:54:39 +00:00