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freebsd-ports/biology
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Mathieu Arnold e1bfdfbe56 Add DOCS options to ports that should have one. 
Also various fixes related to said option.

PR:		230864
Submitted by:	mat
exp-runs by:	antoine
2018-09-10 13:14:50 +00:00
..
artemis biology/artemis: Update 9 -> 17.0.1-11 2018-06-11 17:45:56 +00:00
avida biology/avida: Fix build with Clang 6 2018-08-25 03:22:18 +00:00
babel
bamtools
bcftools biology/bcftools: update to 1.9 2018-08-02 19:30:57 +00:00
bedtools biology/bedtools: Fix Makefile to respect PREFIX 2018-06-16 17:55:01 +00:00
biococoa
bowtie Add DOCS options to ports that should have one. 2018-09-10 13:14:50 +00:00
bowtie2
bwa
canu devel/boost-*: update to 1.68.0 2018-08-09 06:58:30 +00:00
cd-hit Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
cdbfasta
chemeq
clustal-omega
clustalw
clustalx Replace bsd.qt.mk by Uses/qt.mk and Uses/qt-dist.mk 2018-06-28 17:39:53 +00:00
consed
cytoscape biology/cytoscape: Fix license 2018-08-12 06:29:51 +00:00
ddocent
diamond
emboss
exonerate New port: biology/exonerate: Generic tool for sequence alignment 2018-07-13 07:02:16 +00:00
fasta
fasta3
fastahack
fastdnaml
fastool
fastqc
fasttree Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
fastx-toolkit
fluctuate
freebayes Mark as broken on aarch64, and, where appropriate, armvX. 2018-06-21 23:52:37 +00:00
garlic
gff2ps
gmap
gperiodic
grappa
hmmer biology/hmmer: update to 3.2.1 2018-07-11 15:15:03 +00:00
htslib biology/htslib: update to 1.9 2018-08-02 19:27:13 +00:00
hyphy
igv New port: biology/igv: Visualization tool for genomic datasets 2018-06-25 23:56:00 +00:00
infernal Add new port: biology/infernal 2018-06-06 15:15:18 +00:00
iolib Mark various ports broken on mips64 and, where appropriate, mips. 2018-07-02 00:47:14 +00:00
iqtree biology/iqtree: Update to version 1.6.7 2018-08-27 01:20:28 +00:00
jalview
jellyfish Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
kallisto Update science/hdf5 to 1.10.2 2018-09-05 22:05:23 +00:00
lagan
lamarc biology/lamarc: Fix build with Clang 6 2018-08-25 03:13:37 +00:00
libgtextutils
libsbml biology/libsbml: Fix build with Clang 6 2018-08-25 03:31:43 +00:00
linux-foldingathome biology/linux-foldingathome: reset maintainer by request 2018-07-27 02:19:43 +00:00
mafft
mapm3
migrate
molden Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
mopac Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
mrbayes
mummer
muscle
ncbi-blast+ Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
ncbi-toolkit
ngs-sdk Mark as broken on aarch64. 2018-06-25 05:04:46 +00:00
njplot
p5-AcePerl
p5-Bio-ASN1-EntrezGene
p5-Bio-Coordinate
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-FeatureIO
p5-Bio-GFF3
p5-Bio-Glite
p5-Bio-Graphics
p5-Bio-MAGETAB
p5-Bio-NEXUS
p5-Bio-Phylo
p5-Bio-SCF
p5-BioPerl
p5-BioPerl-Run
p5-transdecoder
p5-TrimGalore
paml
pbbam devel/boost-*: update to 1.68.0 2018-08-09 06:58:30 +00:00
pbcopper devel/boost-*: update to 1.68.0 2018-08-09 06:58:30 +00:00
pbseqan
pear-merger Mark as broken on aarch64, and, where appropriate, armvX. 2018-06-21 23:52:37 +00:00
phrap Add DOCS options to ports that should have one. 2018-09-10 13:14:50 +00:00
phred Add DOCS options to ports that should have one. 2018-09-10 13:14:50 +00:00
phylip
phyml biology/phyml: update to v3.3.20180621 2018-06-23 15:53:54 +00:00
plinkseq
primer3 biology/primer3: Fix build with Clang 6 2018-08-25 03:35:46 +00:00
protomol biology/protomol: Fix doubled USES overwriting the old value 2018-08-25 03:47:25 +00:00
psi88 Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
py-biom-format Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
py-biopython - Update to 1.72 2018-08-24 00:12:38 +00:00
py-bx-python biology/py-bx-python: Update 0.8.1 -> 0.8.2 2018-08-26 09:50:41 +00:00
py-cutadapt Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
py-Genesis-PyAPI Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
py-macs2
py-orange3-bioinformatics biology/py-orange3-bioinformatics: Update 3.1.1 -> 3.2.0 2018-08-09 00:29:50 +00:00
py-orange3-single-cell biology/py-orange3-single-cell: Update 0.7.0 -> 0.8.0 2018-08-08 23:08:51 +00:00
py-pysam biology/py-pysam: Update 0.14.1 -> 0.15.0 2018-07-30 19:47:49 +00:00
pycogent Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
pyfasta
python-nexus
rainbow
recombine
ruby-bio
rubygem-bio
samtools biology/samtools: update to 1.9 2018-08-02 19:28:36 +00:00
seaview biology/seaview: Fix build with Clang 6 2018-09-08 09:01:35 +00:00
seqan
seqan1
seqan-apps devel/boost-*: update to 1.68.0 2018-08-09 06:58:30 +00:00
seqio
seqtk
seqtools
sim4
slclust
smithwaterman
stacks biology/stacks: Enable OpenMP (oversight in previous commit) 2018-09-01 14:14:11 +00:00
stringtie New port: biology/stringtie: Transcript assembly and quantification for RNA-seq 2018-07-11 21:32:39 +00:00
t_coffee Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
tabixpp
tinker Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
treepuzzle
trimadap Mark as broken on aarch64, and, where appropriate, armvX. 2018-06-21 23:52:37 +00:00
trimmomatic
tRNAscan-SE Mark BROKEN: missing plist 2018-06-29 12:43:19 +00:00
ugene Update to 1.31.0 2018-09-02 20:47:15 +00:00
unanimity biology/unanimity: Upgrade to latest release, soften dep version requirements 2018-08-25 22:54:54 +00:00
vcflib Mark these ports as broken on aarch64. 2018-06-22 00:03:08 +00:00
vcftools biology/vcftools: Update to 0.1.16, a security release 2018-08-04 01:29:29 +00:00
velvet
wise
xmolwt
Makefile Remove expired ports: 2018-08-16 20:28:32 +00:00