Eitan Adler 9be317dee3 biology/linux-foldingathome: reset maintainer by request ... Jonatan lacks the time to maintain the port. Thank you for your help so far, and you're welcome back any time. Approved by: onatan@gmail.com (maintainer)		2018-07-27 02:19:43 +00:00
..
artemis	biology/artemis: Update 9 -> 17.0.1-11	2018-06-11 17:45:56 +00:00
avida
babel
bamtools
bcftools	Update math/gsl to 2.5	2018-06-23 08:27:13 +00:00
bedtools	biology/bedtools: Fix Makefile to respect PREFIX	2018-06-16 17:55:01 +00:00
biococoa
blat	Deprecate unmaintained ports under the NONE license	2018-07-13 09:56:57 +00:00
bowtie
bowtie2
bwa
canu	Mark as broken on aarch64, and, where appropriate, armvX.	2018-06-21 23:52:37 +00:00
cd-hit
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	New port: biology/cytoscape: Software to visualize molecular interaction networks, gene expression	2018-07-03 08:42:54 +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
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 1.6 -> 1.8	2018-07-16 18:11:44 +00:00
hyphy
igv	New port: biology/igv: Visualization tool for genomic datasets	2018-06-25 23:56:00 +00:00
infernal
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 1.6.6	2018-07-08 21:15:47 +00:00
jalview
jellyfish
kallisto
lagan
lamarc
libgtextutils
libsbml	- Update to 5.17.0	2018-06-25 01:37:52 +00:00
linux-foldingathome	biology/linux-foldingathome: reset maintainer by request	2018-07-27 02:19:43 +00:00
mafft
mapm3
migrate
molden	biology/molden: Unbreak by updating the MASTER_SITES URL	2018-07-20 09:44:14 +00:00
mopac
mrbayes
mummer
muscle
ncbi-blast+
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
pbcopper
pbseqan
pear-merger	Mark as broken on aarch64, and, where appropriate, armvX.	2018-06-21 23:52:37 +00:00
phrap
phred
phylip
phyml	biology/phyml: update to v3.3.20180621	2018-06-23 15:53:54 +00:00
plinkseq
primer3
protomol
psi88
py-biom-format	Use PY_FLAVOR for dependencies.	2018-06-20 17:05:41 +00:00
py-biopython	Use PY_FLAVOR for dependencies.	2018-06-20 17:05:41 +00:00
py-bx-python	Use PY_FLAVOR for dependencies.	2018-06-20 17:05:41 +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 3.1.0 -> 3.1.1	2018-07-12 20:09:38 +00:00
py-pysam
pycogent	Use PY_FLAVOR for dependencies.	2018-06-20 17:05:41 +00:00
pyfasta
python-nexus
rainbow
recombine
ruby-bio
rubygem-bio
samtools
seaview	biology/seaview: Updatye version 4.6.5=>4.7	2018-07-22 03:22:15 +00:00
seqan
seqan1
seqan-apps	Mark as broken on powerpc64 pending fix for PR 199603.	2018-06-18 19:14:48 +00:00
seqio
seqtk
seqtools
sim4
slclust
smithwaterman
stacks	Adjust USES to fix builds on gcc-based architectures.	2018-06-18 19:03:03 +00:00
stringtie	New port: biology/stringtie: Transcript assembly and quantification for RNA-seq	2018-07-11 21:32:39 +00:00
t_coffee
tabixpp
tinker
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	Replace bsd.qt.mk by Uses/qt.mk and Uses/qt-dist.mk	2018-06-28 17:39:53 +00:00
unanimity	Mark these ports as broken on aarch64.	2018-06-22 00:03:08 +00:00
vcflib	Mark these ports as broken on aarch64.	2018-06-22 00:03:08 +00:00
vcftools
velvet
wise
xmolwt
Makefile	New port: biology/exonerate: Generic tool for sequence alignment	2018-07-13 07:02:16 +00:00