Kyle Evans 349be39472 biology/paml: fix the build with LLVM 11 ... LLVM 11 switched from -fcommon to -fno-common by default. This revealed a slight misposition of names in paml.h, which caused one symbol per enum that's not used anywhere. The fix just moves the names back so that the enums are named that, rather than creating new unused symbols. Reviewed by: zeising Approved by: jrm (maintainer) MFH: 2020Q3		2020-08-20 17:07:03 +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
canu
cd-hit
cdbfasta
checkm
clustal-omega
clustalw
cufflinks	biology/htslib: Upgrade to 1.10.2	2020-08-03 17:40:04 +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
groopm	biology/groopm: Remove python's 2.7 restriction placed here by mistake	2020-08-13 19:19:23 +00:00
haplohseq
hhsuite
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
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+
ncbi-cxx-toolkit
ncbi-toolkit
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
pbcopper	Deprecate ports broken for more than 6 months	2020-07-26 07:32:00 +00:00
pbseqan
pear-merger
phrap
phred
phylip
phyml	biology/phyml: update to 3.3.20200621	2020-07-10 09:45:48 +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
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
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 deprecated ports:	2020-08-15 10:50:58 +00:00