Joseph Mingrone bc66849a97 biology/diamond: Update to version 2.0.4 ... Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v2.0.3 https://github.com/bbuchfink/diamond/releases/tag/v2.0.4 Port changes: Remove a patch that was upstreamed: https://github.com/bbuchfink/diamond/pull/378		2020-08-30 16:14:22 +00:00
..
abyss
artemis
avida
babel
bamtools
bcftools
bedtools
bioawk
biococoa
bolt-lmm
bowtie
bowtie2
bwa	biology/bwa: fix build on recent current	2020-08-28 11:17:13 +00:00
canu
cd-hit
cdbfasta
checkm
clustal-omega
clustalw
cufflinks	biology/cufflinks: fix build on recent current	2020-08-28 18:24:04 +00:00
cytoscape
ddocent
diamond	biology/diamond: Update to version 2.0.4	2020-08-30 16:14:22 +00:00
dsr-pdb
emboss
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastp
fastqc
fasttree
fastx-toolkit
figtree
fluctuate
freebayes
garlic
gatk
gcta
gemma
gff2ps
gmap
gperiodic
graphlan	biology/graphlan: Remove the 2.7 limitation on python because it's no longer needed	2020-08-14 04:59:29 +00:00
grappa	Extend expiration of ports broken with -fno-common	2020-08-30 09:47:49 +00:00
groopm	biology/groopm: Remove python's 2.7 restriction placed here by mistake	2020-08-13 19:19:23 +00:00
haplohseq
hhsuite	biology/hhsuite: Update 3.2.0 -> 3.3.0	2020-08-27 04:28:24 +00:00
hisat2
hmmer
htslib
hyphy	biology/hyphy: Update to version 2.5.17	2020-08-20 16:15:22 +00:00
igv
infernal
iolib
iqtree
jalview
jellyfish
kallisto
lagan	Extend expiration of ports broken with -fno-common	2020-08-30 09:47:49 +00:00
lamarc
libbigwig
libgtextutils
libsbml
linux-foldingathome
mafft
mapm3
migrate
minimap2
molden
mopac
mothur
mrbayes
mummer
muscle
ncbi-blast+	Chase security/p11-kit update	2020-08-30 03:10:23 +00:00
ncbi-cxx-toolkit
ncbi-toolkit	Chase security/p11-kit update	2020-08-30 03:10:23 +00:00
ngs-sdk
p5-AcePerl
p5-Bio-ASN1-EntrezGene
p5-Bio-Cluster
p5-Bio-Coordinate
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-DB-EMBL
p5-Bio-DB-NCBIHelper
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-Bio-Variation
p5-BioPerl
p5-BioPerl-Run
p5-transdecoder
p5-TrimGalore
paml	biology/paml: fix the build with LLVM 11	2020-08-20 17:07:03 +00:00
pbbam
pbseqan
pear-merger
phrap
phred
phylip	Extend expiration of ports broken with -fno-common	2020-08-30 09:47:49 +00:00
phyml	biology/phyml: fix build on recent current	2020-08-29 08:34:27 +00:00
picard-tools	biology/picard-tools: Remove extraneous file	2020-08-30 14:06:54 +00:00
plink
primer3
prodigal
prodigy-lig
protomol
psi88
py-biopython
py-bx-python
py-cutadapt
py-dnaio
py-ete3
py-fastTSNE
py-Genesis-PyAPI
py-gffutils
py-gtfparse
py-hits
py-loompy
py-macs2
py-multiqc
py-orange3-bioinformatics
py-orange3-single-cell
py-pandas-charm
py-pyfaidx
py-pysam
py-scikit-bio	devel/ipython: Update to 7.17.0	2020-08-15 12:50:57 +00:00
py-xenaPython
pyfasta
python-nexus
rainbow
recombine
ruby-bio
rubygem-bio
rubygem-bio-executables
rubygem-bio-old-biofetch-emulator
rubygem-bio-shell
samtools
scrm
seaview
seqan
seqan1
seqan-apps
seqio
seqtk
sim4
slclust
smithwaterman
stacks
star
stringtie
subread
tabixpp
tophat
treekin
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ugene
vcflib
vcftools
velvet
viennarna
vsearch
vt
wise
Makefile	Remove expired ports:	2020-08-27 11:25:47 +00:00