Yuri Victorovich 377565226d biology/tinker: Update 7.1.3 -> 8.4.4; Move to science/ ... Port changes: * Take maintainership * Implement the 'benchmarks' target, and stop installing benchmarks * Add USES=gmake * Update license * Change MASTER_SITES and WWW to https * Silence some commands		2018-10-07 00:19:22 +00:00
..
artemis
avida
babel
bamtools
bcftools
bedtools	Fix build on gcc-based archs by updating USES.	2018-09-22 05:30:31 +00:00
biococoa	Update Objective-C LLVM version to 6.0.	2018-09-26 15:23:37 +00:00
bowtie	Add DOCS options to ports that should have one.	2018-09-10 13:14:50 +00:00
bowtie2	Update devel/tbb to version 2019 and bump dependent port's revisions	2018-10-04 10:03:59 +00:00
bwa
canu
cd-hit
cdbfasta
chemeq
clustal-omega
clustalw
clustalx
consed
cytoscape
ddocent
diamond
emboss
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastqc
fasttree
fastx-toolkit
fluctuate
freebayes	Upgrade these ports to USES=compiler:c++11-lang to fix build on gcc-based	2018-09-18 09:28:34 +00:00
garlic
gff2ps
gmap
gperiodic
grappa
hmmer
htslib
hyphy
igv
infernal	Allow building on powerpc64.	2018-09-27 23:02:56 +00:00
iolib	- Update to 1-14-10	2018-09-28 18:47:49 +00:00
iqtree
jalview
jellyfish
kallisto
lagan
lamarc
libgtextutils
libsbml
linux-foldingathome
mafft
mapm3
migrate
molden
mopac
mrbayes
mummer
muscle
ncbi-blast+
ncbi-toolkit
ngs-sdk	biology/ngs-sdk: Update 2.9.1 -> 2.9.2	2018-09-19 18:09:37 +00:00
njplot
p5-AcePerl	Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except	2018-10-06 13:06:42 +00:00
p5-Bio-ASN1-EntrezGene	Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except	2018-10-06 13:06:42 +00:00
p5-Bio-Coordinate	Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except	2018-10-06 13:06:42 +00:00
p5-Bio-Das	Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except	2018-10-06 13:06:42 +00:00
p5-Bio-Das-Lite	Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except	2018-10-06 13:06:42 +00:00
p5-Bio-FeatureIO	Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except	2018-10-06 13:06:42 +00:00
p5-Bio-GFF3	Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except	2018-10-06 13:06:42 +00:00
p5-Bio-Glite	Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except	2018-10-06 13:06:42 +00:00
p5-Bio-Graphics	Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except	2018-10-06 13:06:42 +00:00
p5-Bio-MAGETAB	Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except	2018-10-06 13:06:42 +00:00
p5-Bio-NEXUS	Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except	2018-10-06 13:06:42 +00:00
p5-Bio-Phylo	Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except	2018-10-06 13:06:42 +00:00
p5-Bio-SCF	Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except	2018-10-06 13:06:42 +00:00
p5-BioPerl	Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except	2018-10-06 13:06:42 +00:00
p5-BioPerl-Run	Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except	2018-10-06 13:06:42 +00:00
p5-transdecoder
p5-TrimGalore
paml
pbbam	More precisely specify USES=compiler to fix build on gcc-based	2018-09-18 08:14:23 +00:00
pbcopper	More precisely specify USES=compiler to fix build on gcc-based	2018-09-18 08:14:23 +00:00
pbseqan
pear-merger
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	Change 4 ports from net/mpich2 to net/mpich	2018-09-22 18:00:24 +00:00
plinkseq
primer3
protomol
psi88
py-biom-format	biology/py-biom-format: Update to version 2.1.7	2018-10-06 15:28:01 +00:00
py-biopython
py-bx-python
py-cutadapt	biology/py-cutadapt: Upgrade to 1.18	2018-09-20 14:10:52 +00:00
py-Genesis-PyAPI
py-loompy	New port: biology/py-loompy: Work with .loom files for single-cell RNA-seq data	2018-09-21 08:04:50 +00:00
py-macs2
py-orange3-bioinformatics
py-orange3-single-cell
py-pysam	biology/py-pysam: Update 0.15.0 -> 0.15.1	2018-09-17 17:40:28 +00:00
pycogent
pyfasta
python-nexus	- Update to 1.63	2018-09-22 08:54:58 +00:00
rainbow
recombine
ruby-bio
rubygem-bio	Update to 1.5.2	2018-09-21 18:08:24 +00:00
samtools
seaview
seqan
seqan1
seqan-apps
seqio
seqtk
seqtools
sim4
slclust
smithwaterman
stacks
stringtie
t_coffee
tabixpp
treepuzzle
trimadap
trimmomatic
tRNAscan-SE	- Unbreak by adding missing pkg-plist	2018-09-28 00:12:48 +00:00
ugene
unanimity	More precisely specify USES=compiler to fix build on gcc-based	2018-09-18 08:14:23 +00:00
vcflib
vcftools
velvet
wise
xmolwt
Makefile	biology/tinker: Update 7.1.3 -> 8.4.4; Move to science/	2018-10-07 00:19:22 +00:00