Yuri Victorovich 1faa8eff29 biology/artemis: Update 9 -> 17.0.1-11 ... Port changes: * Take maintainership * Change to github * Change to DISTVERSION * Add LICENSE * Depends on bash * Add USES=gmake * Remove NO_BUILD: needs to build jars from java files * Update the post-extract target * Change do-install to do minimal installation * Update WWW		2018-06-11 17:45:56 +00:00
..
artemis	biology/artemis: Update 9 -> 17.0.1-11	2018-06-11 17:45:56 +00:00
avida
babel
bamtools	biology/bamtools: API and toolkit for handling BAM files	2018-03-28 13:26:31 +00:00
bcftools
bedtools	biology/bedtools: Upgrade to 2.27.1	2018-04-19 16:44:59 +00:00
biococoa
blat
bowtie
bowtie2
bwa
canu	biology/canu: Upgrade to 1.7 release	2018-04-26 04:16:15 +00:00
cd-hit
cdbfasta
chemeq
clustal-omega	biology/clustal-omega: Multiple alignment of nucleic acid and protein, replaces clustalw	2018-05-21 22:15:26 +00:00
clustalw	biology/clustalw: Fix license, take maintainership	2018-05-21 01:13:40 +00:00
clustalx	biology/clustalx: Multiple alignment of nucleic acid and protein sequences with GUI	2018-05-21 20:56:17 +00:00
consed
ddocent	biology/ddocent: Bash pipeline for RAD sequencing	2018-04-20 01:34:05 +00:00
diamond	biology/diamond: Update to version 0.9.22	2018-05-14 17:17:11 +00:00
emboss
fasta
fasta3
fastahack	biology/fastahack: Utility for indexing and sequence extraction from FASTA files	2018-04-16 14:50:46 +00:00
fastdnaml
fastool
fastqc
fasttree
fastx-toolkit	biology/fastx-toolkit: Fix build on FreeBSD 12	2018-05-16 15:13:43 +00:00
fluctuate
freebayes	biology/freebayes: Bayesian haplotype-based polymorphism discovery and genotyping	2018-04-20 00:07:27 +00:00
garlic
gff2ps
gmap
gperiodic
grappa
hmmer
htslib
hyphy	biology/hyphy: Update to version 2.3.13	2018-05-22 22:55:18 +00:00
infernal	Add new port: biology/infernal	2018-06-06 15:15:18 +00:00
iolib
iqtree	biology/iqtree: Update to version 1.6.5	2018-05-11 16:57:09 +00:00
jalview
jellyfish
kallisto	Adjust USES to fix building on gcc-based archs (in particular, powerpc64).	2018-06-02 19:40:59 +00:00
lagan
lamarc
libgtextutils	biology/libgtextutils: Unbreak for FreeBSD 12	2018-03-29 15:41:07 +00:00
libsbml
linux-foldingathome
mafft
mapm3
migrate
molden	biolog/molden: unbreak after at least two intransparent distfile updates	2018-05-20 21:41:57 +00:00
mopac
mrbayes
mummer
muscle
ncbi-blast+	Mark as broken on powerpc64. The entire, unhelpful, error message is:	2018-06-03 11:14:53 +00:00
ncbi-toolkit
ngs-sdk	New port: biology/ngs-sdk: Tools and libraries for using data in the INSDC Sequence Read Archives	2018-06-10 23:58:07 +00:00
njplot
p5-AcePerl	Update WWW	2018-05-27 20:15:16 +00:00
p5-Bio-ASN1-EntrezGene	Update WWW	2018-05-27 20:15:16 +00:00
p5-Bio-Coordinate	Update WWW	2018-05-27 20:15:16 +00:00
p5-Bio-Das	Update WWW	2018-05-27 20:15:16 +00:00
p5-Bio-Das-Lite	Update WWW	2018-05-27 20:15:16 +00:00
p5-Bio-FeatureIO	Update WWW	2018-05-27 20:15:16 +00:00
p5-Bio-GFF3	Update WWW	2018-05-27 20:15:16 +00:00
p5-Bio-Glite	Update WWW	2018-05-27 20:15:16 +00:00
p5-Bio-Graphics	Update WWW	2018-05-27 20:15:16 +00:00
p5-Bio-MAGETAB	Update WWW	2018-05-27 20:15:16 +00:00
p5-Bio-NEXUS	Update WWW	2018-05-27 20:15:16 +00:00
p5-Bio-Phylo	Update WWW	2018-05-27 20:15:16 +00:00
p5-Bio-SCF	Update WWW	2018-05-27 20:15:16 +00:00
p5-BioPerl
p5-BioPerl-Run
p5-transdecoder
p5-TrimGalore
paml	biology/paml: Set PORTVERSION directly	2018-04-26 15:36:30 +00:00
pbbam	biology/pbbam: PacBio BAM C++ library, with SWIG bindings	2018-04-23 16:08:21 +00:00
pbcopper	biology/pbcopper: Core C++ library for Pacific Biosciences tools	2018-04-23 16:23:53 +00:00
pbseqan	biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn	2018-04-21 17:21:30 +00:00
pear-merger	biology/pear-merger: Memory-efficient and accurate paired-end read merger	2018-04-04 17:21:39 +00:00
phrap
phred
phylip
phyml	- Update to 3.3.20180214	2018-05-15 03:17:54 +00:00
plinkseq
primer3
protomol
psi88
py-biom-format
py-biopython	biology/py-biopython: Unbreak on python3; Add license	2018-05-13 22:30:00 +00:00
py-bx-python
py-cutadapt	Switch all pypi.python.org WWWs to a new PyPi home pypi.org where	2018-04-25 16:42:37 +00:00
py-macs2
py-pysam	Switch all pypi.python.org WWWs to a new PyPi home pypi.org where	2018-04-25 16:42:37 +00:00
pycogent
pyfasta
python-nexus	- Update to 1.61	2018-04-01 11:52:08 +00:00
rainbow	biology/rainbow: Efficient clustering and assembling of short reads	2018-04-02 16:50:46 +00:00
recombine
ruby-bio
rubygem-bio
samtools
seaview	biology/seaview: Update version 4.6.3=>4.6.5	2018-04-24 12:31:32 +00:00
seqan
seqan1
seqan-apps	devel/boost-*: update to 1.67.0	2018-04-18 13:57:42 +00:00
seqio
seqtk	biology/seqtk: Tool for processing sequences in FASTA/FASTQ format	2018-04-03 20:57:05 +00:00
seqtools
sim4
slclust
smithwaterman	biology/smithwaterman: Smith-waterman-gotoh alignment algorithm	2018-04-15 17:45:52 +00:00
stacks	biology/stacks: Software pipeline for building loci from short-read sequences	2018-03-31 13:16:05 +00:00
t_coffee
tabixpp	biology/tabixpp: C++ wrapper to tabix indexer	2018-04-14 23:52:16 +00:00
tinker
treepuzzle
trimadap	biology/trimadap: Trim adapter sequences from Illumina data	2018-04-03 18:23:54 +00:00
trimmomatic
tRNAscan-SE	Update to 2.0.0 and pass maintainership to committer.	2018-06-06 15:20:57 +00:00
ugene	Add upstream patch to fix the build with Qt 5.10.	2018-05-15 18:51:51 +00:00
unanimity	biology/unanimity: Pacific Biosciences consensus library and applications	2018-04-24 14:16:46 +00:00
vcflib	biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF files	2018-04-17 03:11:39 +00:00
vcftools
velvet
wise
xmolwt
Makefile	New port: biology/ngs-sdk: Tools and libraries for using data in the INSDC Sequence Read Archives	2018-06-10 23:58:07 +00:00