Piotr Kubaj 4c1ed61171 biology/mummer: fix build on powerpc64 elfv2 and powerpc64le ... Error: src/tigr/postnuc.cc:174:37: error: non-constant-expression cannot be narrowed from type 'signed char' to 'char' in initializer list [-Wc++11-narrowing] Alignments.push_back({ *Mp, CurrCp->dirB } ); Since it may also fix runtime issues on powerpc64 elfv1, bump PORTREVISION.		2020-10-25 23:03:14 +00:00
..
abyss	biology/abyss: Update 2.2.4 -> 2.2.5	2020-09-27 06:59:05 +00:00
artemis
avida
babel
bamtools
bcftools
bedtools
bioawk
biococoa
bolt-lmm	Canonicalize powerpc64le CXXFLAGS to be the same as powerpc64.	2020-09-27 07:41:33 +00:00
bowtie
bowtie2
bwa	biology/bwa: fix build on recent current	2020-08-28 11:17:13 +00:00
canu	biology/canu: Upgrade to 2.1	2020-09-14 22:27:37 +00:00
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	Fix build with -fno-common	2020-09-21 18:14:57 +00:00
garlic
gatk	biology/gatk: Fix build	2020-09-08 19:25:36 +00:00
gcta
gemma
gff2ps
gmap	biology/gmap: enable on powerpc64le	2020-10-09 13:23:12 +00:00
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
hhsuite	biology/hhsuite: Update 3.2.0 -> 3.3.0	2020-08-27 04:28:24 +00:00
hisat2
hmmer	Also enable on powerpc64le.	2020-09-24 20:29:35 +00:00
htslib
hyphy	biology/hyphy: Update to version 2.5.20	2020-10-16 23:43:17 +00:00
igv
infernal	Also enable on powerpc64le.	2020-09-24 20:38:59 +00:00
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	Convert REINPLACE_CMD to patch file	2020-09-29 18:23:04 +00:00
linux-foldingathome
mafft
mapm3	biology/mapm3: Reformat patches.	2020-09-04 12:24:23 +00:00
migrate
minimap2
molden
mopac
mothur	biology/mothur: fix build on powerpc64le	2020-10-19 10:30:11 +00:00
mrbayes
mummer	biology/mummer: fix build on powerpc64 elfv2 and powerpc64le	2020-10-25 23:03:14 +00:00
muscle
ncbi-blast+	Chase security/p11-kit update	2020-08-30 03:10:23 +00:00
ncbi-cxx-toolkit	biology/ncbi-cxx-toolkit: Fix build on 13	2020-09-27 04:57:44 +00:00
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	Allow building on powerpc64le.	2020-09-27 07:44:15 +00:00
primer3
prodigal
prodigy-lig
protomol
psi88
py-biom-format	biology/py-biom-format: Fix fetch and relax scipy requirement	2020-09-26 09:10:37 +00:00
py-biopython	biology/py-biopython: Upgrade to 1.78	2020-10-16 19:12:43 +00:00
py-bx-python
py-cutadapt
py-dnaio
py-ete3	Update PyQt to 5.15.0, py-sip to 4.19.24 and qscintilla2 to 2.11.5	2020-10-05 15:50:03 +00:00
py-fastTSNE
py-Genesis-PyAPI
py-gffutils
py-gtfparse	biology/py-gtfparse: Update 1.2.0 -> 1.2.1	2020-08-07 04:13:00 +00:00
py-hits
py-loompy
py-macs2
py-multiqc	Unbreak bulk -a	2020-09-19 14:15:42 +00:00
py-orange3-bioinformatics
py-orange3-single-cell
py-pandas-charm
py-pyfaidx	biology/py-pyfaidx: Update 0.5.5.2 -> 0.5.9.1	2020-09-13 19:05:30 +00:00
py-pysam
py-scikit-bio	biology/py-scikit-bio: Fix build on the i386 architecture	2020-09-24 23:16:26 +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	biology/subread: Add -fcommon for clang 11	2020-09-18 00:57:35 +00:00
tabixpp
treekin
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ugene
vcflib
vcftools
velvet
viennarna	biology/viennarna: Update 2.4.14 -> 2.4.15	2020-09-07 21:49:07 +00:00
vsearch
vt
wise
Makefile	biology/py-biom-format: Restore in preparation for an update to v2.1.8	2020-09-24 19:31:43 +00:00