Roman Bogorodskiy 8ccd925b80 Chase security/p11-kit update ... After switch to meson libp11-kit.so no longer has symbols in the LIBP11_KIT_1.0 namespace. As a workaround, bump PORTREVISION of consumers to get those rebuilt. See more details in the comments of the linked PR. PR: 248819 Reported by: John Hein		2020-08-30 03:10:23 +00:00
..
abyss	Chanse update of devel/libffi	2020-07-04 18:11:42 +00:00
artemis
avida
babel
bamtools	Bump devel/jsoncpp consumers after r540853.	2020-06-30 17:46:18 +00:00
bcftools	biology/bcftools: Upgrade to 1.10.2	2020-08-03 18:16:54 +00:00
bedtools
bioawk	biology/bioawk: BWK awk modified for biological data	2020-06-05 02:45:33 +00:00
biococoa
bolt-lmm
bowtie	biology/bowtie: Unbreak build with GCC 10	2020-07-04 10:46:08 +00:00
bowtie2	Update devel/tbb to 2020.3 and bump dependent ports' revisions	2020-07-17 10:12:25 +00:00
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 2.0.2	2020-08-07 11:20:11 +00:00
dsr-pdb
emboss
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastp
fastqc
fasttree
fastx-toolkit
figtree
fluctuate
freebayes
garlic
gatk	biology/gatk: Update 4.1.7.0 -> 4.1.8.0	2020-07-09 00:40:56 +00:00
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	biology/: Fix build with clang11 and deprecate ports@ ports	2020-08-29 08:34:51 +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	biology/htslib: Upgrade to 1.10.2	2020-08-03 17:40:04 +00:00
hyphy	biology/hyphy: Update to version 2.5.17	2020-08-20 16:15:22 +00:00
igv
infernal
iolib
iqtree	biology/iqtree: Update to version 2.0.6	2020-05-30 18:43:26 +00:00
jalview
jellyfish	biology/htslib: Upgrade to 1.10.2	2020-08-03 17:40:04 +00:00
kallisto	biology/kallisto: Revert to 0.46.1	2020-08-03 15:45:21 +00:00
lagan	biology/: Fix build with clang11 and deprecate ports@ ports	2020-08-29 08:34:51 +00:00
lamarc
libbigwig
libgtextutils
libsbml	Move devel/swig30 to devel/swig and update to 4.0.1	2020-06-17 18:17:45 +00:00
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	Move devel/p5-IO-stringy to devel/p5-IO-Stringy and update to 2.113	2020-06-26 11:55:23 +00:00
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	biology/htslib: Upgrade to 1.10.2	2020-08-03 17:40:04 +00:00
pbseqan
pear-merger
phrap	Sanitize COMMENT per Section 5.6 of the FreeBSD Porter's Handbook (part 1).	2020-05-27 11:59:13 +00:00
phred
phylip	biology/: Fix build with clang11 and deprecate ports@ ports	2020-08-29 08:34:51 +00:00
phyml	biology/phyml: fix build on recent current	2020-08-29 08:34:27 +00:00
picard-tools	biology/picard-tools: CLI tools for manipulating sequencing data	2020-06-13 13:54:47 +00:00
plink
primer3
prodigal
prodigy-lig	Unbreak bulk -a	2020-06-13 15:05:44 +00:00
protomol
psi88	biology/psi88: Unbreak build with GCC 10	2020-07-04 12:15:58 +00:00
py-biopython	biology/py-biopython: Set python requirement to 3.6+	2020-06-13 13:42:12 +00:00
py-bx-python	biology/py-bx-python: Update 0.8.8 -> 0.8.9	2020-06-26 04:17:11 +00:00
py-cutadapt
py-dnaio	biology/py-dnaio: Upgrade to 0.4.2	2020-05-24 15:23:15 +00:00
py-ete3
py-fastTSNE
py-Genesis-PyAPI
py-gffutils	Unbreak bulk -a	2020-07-14 07:59:28 +00:00
py-gtfparse	biology/py-gtfparse: Update 1.2.0 -> 1.2.1	2020-08-07 04:13:00 +00:00
py-hits
py-loompy	biology/py-loompy: Update 2.0.17 -> 3.0.6	2020-06-16 02:26:08 +00:00
py-macs2
py-multiqc
py-orange3-bioinformatics
py-orange3-single-cell
py-pandas-charm	Clean up some things	2020-05-30 00:57:02 +00:00
py-pyfaidx
py-pysam	biology/py-pysam: Update 0.15.4 -> 0.16.0	2020-06-09 05:03:48 +00:00
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	Update to 2.0.1	2020-07-24 07:49:43 +00:00
rubygem-bio-executables	Add rubygem-bio-executables 1.0.0	2020-07-24 07:08:00 +00:00
rubygem-bio-old-biofetch-emulator	Add rubygem-bio-old-biofetch-emulator 1.0.0	2020-07-24 07:08:05 +00:00
rubygem-bio-shell	Add rubygem-bio-shell 1.0.0	2020-07-24 07:08:11 +00:00
samtools	biology/samtools: Upgrade to 1.10	2020-08-03 18:22:06 +00:00
scrm
seaview	biology/seaview: Update version 5.0.3=>5.0.4	2020-06-22 17:34:44 +00:00
seqan
seqan1
seqan-apps
seqio
seqtk
sim4
slclust
smithwaterman
stacks
star
stringtie
subread	biology/subread: Read alignment, quantification and mutation discovery	2020-06-05 01:55:49 +00:00
tabixpp	biology/htslib: Upgrade to 1.10.2	2020-08-03 17:40:04 +00:00
tophat
treekin
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ugene
vcflib	biology/htslib: Upgrade to 1.10.2	2020-08-03 17:40:04 +00:00
vcftools
velvet
viennarna
vsearch	biology/vsearch: Update to 2.15.0	2020-06-20 14:31:59 +00:00
vt	biology/vt: Patch to work with htslib 1.10.2	2020-08-03 17:42:32 +00:00
wise
Makefile	Remove expired ports:	2020-08-27 11:25:47 +00:00