Johannes M Dieterich 7feb3fa279 biology/molden: update to 5.8.2 ... Also add do-install-{option}-on targets and shadow ${MKDIR} commands. PR: 233060 Submitted by: yuri		2018-11-13 07:03:15 +00:00
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artemis
avida
babel
bamtools
bcftools
bedtools
biococoa
bowtie	biology/bowtie: Patch for gcc8 and clean up	2018-11-03 23:24:29 +00:00
bowtie2	Update devel/tbb to version 2019.1 and bump dependent ports' revisions	2018-10-11 14:47:13 +00:00
bwa
canu	biology/canu: Upgrade to 1.8, add experimental SLURM integration	2018-11-04 14:29:02 +00:00
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
garlic
gff2ps
gmap
gperiodic
grappa
hmmer
htslib
hyphy	biology/hyphy: Update to version 2.3.14.16	2018-10-20 12:21:15 +00:00
igv	biology/igv: Update 2.4.10 -> 2.4.15	2018-11-04 22:55:24 +00:00
infernal
iolib	Remove the incorrect typedefs to fix build on tier-2.	2018-11-05 19:45:23 +00:00
iqtree	biology/iqtree: Update to version 1.6.8	2018-10-28 22:00:18 +00:00
jalview
jellyfish
kallisto
lagan
lamarc
libgtextutils
libsbml
linux-foldingathome
mafft
mapm3
migrate
molden	biology/molden: update to 5.8.2	2018-11-13 07:03:15 +00:00
mopac
mrbayes
mummer
muscle
ncbi-blast+
ncbi-cxx-toolkit
ncbi-toolkit	Fix build failure with base GCC because of double typedefs.	2018-11-05 19:47:42 +00:00
ngs-sdk	biology/ngs-sdk: Update 2.9.2 -> 2.9.3	2018-10-18 21:38:21 +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	biology/p5-transdecoder: Upgrade to 5.4.0	2018-10-23 12:51:20 +00:00
p5-TrimGalore
paml
pbbam
pbcopper
pbseqan
pear-merger
phrap
phred
phylip
phyml
plinkseq
primer3
protomol
psi88
py-biom-format
py-biopython
py-bx-python
py-cutadapt
py-Genesis-PyAPI
py-gffutils	New port: biology/py-gffutils: Work with GFF and GTF files in a flexible database framework	2018-10-19 02:06:53 +00:00
py-gtfparse	New port: biology/py-gtfparse: Parsing tools for GTF (gene transfer format) files	2018-10-19 02:03:40 +00:00
py-loompy	biology/py-loompy: Update 2.0.15 -> 2.0.16	2018-10-30 05:57:43 +00:00
py-macs2
py-orange3-bioinformatics	biology/py-orange3-bioinformatics: Update 3.2.0 -> 3.2.2	2018-10-14 03:22:49 +00:00
py-orange3-single-cell	biology/py-orange3-single-cell: Update 0.8.1 -> 0.8.2	2018-10-17 07:31:34 +00:00
py-pyfaidx	biology/py-pyfaidx: Update 0.5.5.1 -> 0.5.5.2	2018-10-28 04:34:14 +00:00
py-pysam
pycogent
pyfasta
python-nexus
rainbow
recombine
ruby-bio
rubygem-bio
samtools
seaview
seqan
seqan1
seqan-apps	biology/seqan-apps: fix build with GCC-based architectures	2018-11-09 21:37:01 +00:00
seqio
seqtk
seqtools
sim4
slclust
smithwaterman
stacks	Fix build with tier-2 arches.	2018-10-28 08:58:00 +00:00
stringtie
t_coffee
tabixpp
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ugene
unanimity
vcflib
vcftools
velvet
wise
xmolwt	Deprecate most glib12 consumers	2018-10-12 09:19:04 +00:00
Makefile	New port: biology/py-gffutils: Work with GFF and GTF files in a flexible database framework	2018-10-19 02:06:53 +00:00