Yuri Victorovich 57ca301450 biology/mothur: Update 1.42.2 -> 1.42.3 ... Reported by: portscout		2019-06-28 04:02:22 +00:00
..
abyss	biology/abyss: fix build on big-endian architectures	2019-06-21 11:43:09 +00:00
artemis
avida
babel
bamtools
bcftools
bedtools
biococoa
bolt-lmm	biology/bolt-lmm: Mixed model association testing and variance component analysis	2019-05-26 03:36:49 +00:00
bowtie
bowtie2	biology/bowtie2: Clarify CPU-specificity	2019-04-24 17:41:27 +00:00
bwa
canu	biology/canu: Fix build on powerpc64 and aarch64	2019-04-18 12:15:56 +00:00
cd-hit
cdbfasta
checkm	Bump a few PORTREVISIONs after r498529	2019-04-10 06:18:31 +00:00
chemeq
clustal-omega
clustalw
consed
cufflinks	biology/cufflinks: Fix build on i386 by removing the hard-coded -m64	2019-05-29 07:02:28 +00:00
cytoscape
ddocent	biology/ddocent: Upgrade to 2.7.8	2019-05-04 15:09:10 +00:00
diamond
dsr-pdb	devel/boost-*: update to 1.70.0	2019-04-12 06:36:31 +00:00
emboss
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastp	biology/fastp: Remove redundant USE_GCC	2019-05-20 23:41:08 +00:00
fastqc
fasttree
fastx-toolkit
figtree
fluctuate
freebayes
garlic
gatk
gemma	biology/gemma: Lowercase PORTNAME, remove unnecesary USE_GCC	2019-05-18 22:41:15 +00:00
gff2ps
gmap	Enable workaround for building on powerpc64.	2019-06-21 11:15:08 +00:00
gperiodic
graphlan
grappa
groopm
hhsuite	biology/hhsuite: Fix build on platforms where SIMD instruction set doesn't exist or isn't detected.	2019-05-22 02:50:56 +00:00
hisat2
hmmer
htslib
hyphy
igv	biology/igv: Update 2.5.2 -> 2.5.3	2019-06-01 20:49:20 +00:00
infernal
iolib	- Fix build in head i386	2019-04-01 19:33:15 +00:00
iqtree	biology/iqtree: Update to version 1.6.11	2019-06-24 21:47:34 +00:00
jalview
jellyfish	biology/jellyfish: Upgrade to 2.2.10, patch for powerpc64	2019-05-13 16:23:35 +00:00
kallisto	biology/kallisto: Upgrade to 0.46.0	2019-06-12 15:24:55 +00:00
lagan
lamarc
libgtextutils
libsbml	Use USES=pathfix	2019-06-22 21:48:14 +00:00
linux-foldingathome
mafft
mapm3
migrate
minimap2	biology/minimap2: Upgrade to 2.17	2019-05-05 14:56:07 +00:00
molden	Related to revision 499061 bump ports with USES=fortran to have them	2019-04-22 13:16:33 +00:00
mopac	Related to revision 499061 bump ports with USES=fortran to have them	2019-04-22 13:16:33 +00:00
mothur	biology/mothur: Update 1.42.2 -> 1.42.3	2019-06-28 04:02:22 +00:00
mrbayes	Update devel/readline to 8.0	2019-04-09 14:04:49 +00:00
mummer
muscle
ncbi-blast+	biology/ncbi-blast+: Fix build on powerpc64, add run dep for update_blastdb.pl	2019-06-14 00:37:59 +00:00
ncbi-cxx-toolkit
ncbi-toolkit
ngs-sdk	Mark this port as not buildable on powerpc64:	2019-06-25 12:17:04 +00:00
p5-AcePerl
p5-Bio-ASN1-EntrezGene
p5-Bio-Cluster
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	Fix typo	2019-04-23 14:11:50 +00:00
p5-Bio-NEXUS
p5-Bio-Phylo
p5-Bio-SCF	- Add LICENSE	2019-03-30 09:01:08 +00:00
p5-BioPerl
p5-BioPerl-Run
p5-transdecoder
p5-TrimGalore	biology/p5-TrimGalore: Upgrade to 0.6.1	2019-03-24 21:44:17 +00:00
paml
pbbam	devel/boost-*: update to 1.70.0	2019-04-12 06:36:31 +00:00
pbcopper	devel/boost-*: update to 1.70.0	2019-04-12 06:36:31 +00:00
pbseqan
pear-merger
phrap
phred
phylip
phyml	- Update to 3.3.20190321	2019-05-20 09:17:29 +00:00
plinkseq
primer3
prodigal
prodigy-lig
protomol
psi88	Related to revision 499061 bump ports with USES=fortran to have them	2019-04-22 13:16:33 +00:00
py-biom-format	Bump a few PORTREVISIONs after r498529	2019-04-10 06:18:31 +00:00
py-biopython
py-bx-python	biology/py-bx-python: Update 0.8.2 -> 0.8.4	2019-06-19 08:08:31 +00:00
py-cutadapt	biology/py-cutadapt: Upgrade to 2.3	2019-04-27 01:26:17 +00:00
py-dnaio	biology/py-dnaio: Read and write FASTQ and FASTA	2019-03-24 19:40:26 +00:00
py-fastTSNE	devel/openmp: phase out	2019-05-08 16:05:53 +00:00
py-Genesis-PyAPI
py-gffutils	Bump a few PORTREVISIONs after r498529	2019-04-10 06:18:31 +00:00
py-gtfparse
py-loompy
py-macs2
py-orange3-bioinformatics
py-orange3-single-cell
py-pyfaidx	Bump a few PORTREVISIONs after r498529	2019-04-10 06:18:31 +00:00
py-pysam
py-xenaPython	New port: biology/py-xenaPython: API for Xena Hub to access genetic information shared through the hub	2019-04-12 17:01:10 +00:00
pycogent
pyfasta
python-nexus
rainbow
recombine
ruby-bio
rubygem-bio
samtools
seaview
seqan
seqan1
seqan-apps	devel/boost-*: update to 1.70.0	2019-04-12 06:36:31 +00:00
seqio
seqtk
seqtools
sim4
slclust
smithwaterman
stacks	biology/stacks: Remove obsolete pkg-message regarding web interface	2019-05-10 21:15:42 +00:00
star	biology/star: Force newer GCC on platforms with GCC 4.2 base	2019-05-02 00:39:51 +00:00
stringtie
t_coffee	Related to revision 499061 bump ports with USES=fortran to have them	2019-04-22 13:16:33 +00:00
tabixpp
treekin	New port: biology/treekin: Efficient computation of RNA folding dynamics	2019-06-15 20:37:06 +00:00
treepuzzle
trimadap	biology/trimadap: Mark only for amd64 and i386	2019-05-11 00:18:24 +00:00
trimmomatic
tRNAscan-SE	biology/tRNAscan-SE: Update to 2.0.3	2019-06-08 01:31:18 +00:00
ugene
unanimity	Clean up plist	2019-04-25 13:25:50 +00:00
vcflib
vcftools
velvet
viennarna	biology/viennarna: Make it less/not prone to failures due to hardcoded C++ library name	2019-06-24 19:30:15 +00:00
vsearch	biology/vsearch: Update to 2.13.4	2019-05-11 13:42:33 +00:00
wise
Makefile	New port: biology/viennarna: Alignment tools for the structural analysis of RNA	2019-06-24 09:29:05 +00:00