Sunpoet Po-Chuan Hsieh 20b6ec5afb Update to 1.007006 (1.7.6) ... - Remove PGTEST and SQLITETEST options: DBD::Pg and DBD::SQLite have been removed from BioPerl by upstream for the move of modules and programs into separate distributions Changes: https://metacpan.org/changes/distribution/BioPerl		2019-09-07 22:44:02 +00:00
..
abyss	devel/boost-*: update to 1.71.0	2019-08-19 15:35:27 +00:00
artemis
avida
babel
bamtools
bcftools	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
bedtools	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
biococoa
bolt-lmm	devel/boost-*: update to 1.71.0	2019-08-19 15:35:27 +00:00
bowtie	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
bowtie2
bwa
canu	devel/boost-*: update to 1.71.0	2019-08-19 15:35:27 +00:00
cd-hit	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
cdbfasta
checkm	biology/checkm: Update 1.0.17 -> 1.0.18	2019-08-19 08:25:29 +00:00
chemeq	Mark BROKEN: unfetchable	2019-08-04 08:31:22 +00:00
clustal-omega
clustalw
consed	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
cufflinks	devel/boost-*: update to 1.71.0	2019-08-19 15:35:27 +00:00
cytoscape
ddocent	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
diamond	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
dsr-pdb	devel/boost-*: update to 1.71.0	2019-08-19 15:35:27 +00:00
emboss	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
exonerate
fasta	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
fasta3	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
fastahack
fastdnaml
fastool
fastp	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
fastqc
fasttree	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
fastx-toolkit
figtree
fluctuate
freebayes	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
garlic
gatk	biology/gatk: Update 4.0.11.0 -> 4.1.2.0-43	2019-07-26 18:03:08 +00:00
gemma	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
gff2ps
gmap	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
gperiodic	biology/gperiodic: fix NLS and other rough edges	2019-08-23 15:26:55 +00:00
graphlan
grappa
groopm	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
hhsuite	biology/hhsuite: fix build on powerpc64	2019-08-05 14:23:23 +00:00
hisat2
hmmer	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
htslib
hyphy	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
igv
infernal
iolib
iqtree	biology/iqtree: Update to version 1.6.12	2019-08-27 01:19:11 +00:00
jalview
jellyfish	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
kallisto	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
lagan	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
lamarc
libbigwig	New port: biology/libbigwig: C library for handling bigWig files (containing genomic data)	2019-07-11 17:05:22 +00:00
libgtextutils
libsbml	Use USES=pathfix	2019-06-22 21:48:14 +00:00
linux-foldingathome	Mark BROKEN: unfetchable	2019-08-04 08:31:22 +00:00
mafft
mapm3
migrate
minimap2
molden	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
mopac	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
mothur	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
mrbayes
mummer	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
muscle
ncbi-blast+	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
ncbi-cxx-toolkit	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
ncbi-toolkit	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
ngs-sdk	biology/ngs-sdk: Update 2.9.6 -> 2.10.0	2019-08-31 15:09:47 +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
p5-Bio-NEXUS
p5-Bio-Phylo
p5-Bio-SCF
p5-BioPerl	Update to 1.007006 (1.7.6)	2019-09-07 22:44:02 +00:00
p5-BioPerl-Run
p5-transdecoder	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
p5-TrimGalore
paml
pbbam	devel/boost-*: update to 1.71.0	2019-08-19 15:35:27 +00:00
pbcopper	devel/boost-*: update to 1.71.0	2019-08-19 15:35:27 +00:00
pbseqan
pear-merger
phrap
phred	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
phylip
phyml
plinkseq
primer3
prodigal
prodigy-lig	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
protomol
psi88	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
py-biom-format	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
py-biopython	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
py-bx-python	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
py-cutadapt
py-dnaio
py-fastTSNE	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
py-Genesis-PyAPI
py-gffutils
py-gtfparse	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
py-loompy	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
py-macs2	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
py-orange3-bioinformatics	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
py-orange3-single-cell	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
py-pyfaidx
py-pysam	biology/py-pysam: Update 0.15.2 -> 0.15.3	2019-08-31 15:49:18 +00:00
py-xenaPython
pycogent	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
pyfasta	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
python-nexus
rainbow
recombine	Fix after gets(3) retirement using gets_s(3).	2019-09-02 05:00:43 +00:00
ruby-bio
rubygem-bio
samtools	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
seaview
seqan
seqan1
seqan-apps	devel/boost-*: update to 1.71.0	2019-08-19 15:35:27 +00:00
seqio
seqtk
seqtools	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
sim4
slclust
smithwaterman
stacks	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
star	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
stringtie
t_coffee	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
tabixpp
treekin	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ugene
unanimity	devel/boost-*: update to 1.71.0	2019-08-19 15:35:27 +00:00
vcflib
vcftools
velvet
viennarna	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
vsearch
wise	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
Makefile	New port: biology/libbigwig: C library for handling bigWig files (containing genomic data)	2019-07-11 17:05:22 +00:00