Jason W. Bacon c904df3468 biology/star: Upgrade to 2.7.2d ... Fix chimeric output bug. Numerous other minor fixes and enhancements since 2.7.0. Reported by: portscout		2019-10-06 22:18:31 +00:00
..
abyss	devel/openmp: update to 9.0.0	2019-09-21 18:59:57 +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	biology/bedtools: Upgrade to 2.29.0	2019-09-13 13:21:59 +00:00
biococoa
bolt-lmm	devel/boost-*: update to 1.71.0	2019-08-19 15:35:27 +00:00
bowtie
bowtie2	Update devel/tbb to 2019.8 and bump dependent ports' revisions	2019-09-25 10:03:49 +00:00
bwa
canu	devel/boost-*: update to 1.71.0	2019-08-19 15:35:27 +00:00
cd-hit
cdbfasta
checkm	biology/checkm: Update 1.0.17 -> 1.0.18	2019-08-19 08:25:29 +00:00
chemeq	Deprecate a few ports	2019-09-15 17:28:08 +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
diamond	biology/diamond: Update to version 0.9.26	2019-09-18 18:45:09 +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	biology/fastahack: Upgrade to 1.0.0	2019-10-06 21:34:32 +00:00
fastdnaml
fastool
fastp
fastqc	biology/fastqc: Upgrade to 0.11.8	2019-09-21 02:44:54 +00:00
fasttree
fastx-toolkit
figtree
fluctuate
freebayes
garlic
gatk
gemma
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
haplohseq	biology/haplohseq: Identify regions of allelic imbalance	2019-09-16 01:07:31 +00:00
hhsuite	devel/openmp: update to 9.0.0	2019-09-21 18:59:57 +00:00
hisat2
hmmer	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
htslib
hyphy
igv
infernal
iolib
iqtree	biology/iqtree: Update to version 1.6.12	2019-08-27 01:19:11 +00:00
jalview
jellyfish	Drop C++11 workaround for GCC < 6 after r449590	2019-09-14 22:01:13 +00:00
kallisto
lagan	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
lamarc
libbigwig
libgtextutils
libsbml
linux-foldingathome	Deprecate a few ports	2019-09-15 17:28:08 +00:00
mafft
mapm3
migrate
minimap2
molden
mopac
mothur	biology/mothur: Update 1.42.3 -> 1.43.0	2019-10-05 17:04:42 +00:00
mrbayes
mummer
muscle
ncbi-blast+
ncbi-cxx-toolkit
ncbi-toolkit	biologi/ncbi-toolkit: Remove dependency on libXp	2019-09-28 10:52:57 +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
p5-TrimGalore	biology/p5-TrimGalore: Upgrade to 0.6.4	2019-09-21 02:51:26 +00:00
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	biology/phyml: update to 3.3.20190909	2019-09-10 21:04:16 +00:00
plinkseq
primer3
prodigal
prodigy-lig
protomol
psi88
py-biom-format
py-biopython
py-bx-python
py-cutadapt	biology/py-cutadapt: Upgrade to 2.5	2019-09-13 13:17:26 +00:00
py-dnaio
py-fastTSNE	devel/openmp: update to 9.0.0	2019-09-21 18:59:57 +00:00
py-Genesis-PyAPI
py-gffutils
py-gtfparse
py-loompy
py-macs2
py-multiqc	biology/py-multiqc: Aggregate bioinformatics analysis reports	2019-09-23 16:09:30 +00:00
py-orange3-bioinformatics
py-orange3-single-cell
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
pyfasta
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	Fix some misspelled or duplicated LICENSE_*	2019-09-17 19:21:45 +00:00
seqan-apps	devel/boost-*: update to 1.71.0	2019-08-19 15:35:27 +00:00
seqio
seqtk
seqtools
sim4
slclust
smithwaterman
stacks
star	biology/star: Upgrade to 2.7.2d	2019-10-06 22:18:31 +00:00
stringtie
t_coffee
tabixpp
tophat	biology/tophat: Fast splice junction mapper for RNA-Seq reads	2019-09-27 00:49:48 +00:00
treekin
treepuzzle
trimadap
trimmomatic	biology/trimmomatic: Upgrade to 0.39	2019-09-14 14:45:49 +00:00
tRNAscan-SE
ugene
unanimity	devel/boost-*: update to 1.71.0	2019-08-19 15:35:27 +00:00
vcflib
vcftools
velvet
viennarna
vsearch
wise	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
Makefile	biology/tophat: Fast splice junction mapper for RNA-Seq reads	2019-09-27 00:49:48 +00:00