Neel Chauhan 1385312c50 Update a few GNUstep ports: ... * devel/gnustep-make: Update to 2.8.0 * lang/gnustep-base: Update to 1.27.0 * x11-toolkits/gnustep-back: update to 0.28.0 * x11-toolkits/gnustep-gui: update to 0.28.0 Also bump PORTREVISION on dependent ports.		2021-02-14 23:21:02 +00:00
..
abyss	biology/abyss: Update 2.2.4 -> 2.2.5	2020-09-27 06:59:05 +00:00
artemis
avida	For ports on riscv64 that fail the same (or similar ways) to aarch64, mark	2021-01-02 01:46:08 +00:00
babel
bamtools
bcftools	biology/bcftools: Upgrade to 1.11	2020-11-05 20:34:03 +00:00
bedtools	biology/bedtools: Upgrade to 2.30.0	2021-01-24 18:25:39 +00:00
bioawk
biococoa	Update a few GNUstep ports:	2021-02-14 23:21:02 +00:00
bioparser	biology/bioparser: Update 3.0.12 -> 3.0.12-2	2021-02-03 19:08:28 +00:00
biosoup	New port: biology/biosoup: Collection of C++ header-only data structures for bioinformatics	2021-01-19 09:01:41 +00:00
bolt-lmm	Canonicalize powerpc64le CXXFLAGS to be the same as powerpc64.	2020-09-27 07:41:33 +00:00
bowtie
bowtie2	biology/bowtie2: Reverse switch to devel/onetbb	2021-01-30 17:43:56 +00:00
bwa	For ports on riscv64 that fail the same (or similar ways) to aarch64, mark	2021-01-02 01:46:08 +00:00
canu	biology/canu: Drop dependency on gcc	2021-01-11 16:51:15 +00:00
cd-hit	biology/cd-hit: Drop dependency on gcc	2021-01-11 16:55:15 +00:00
cdbfasta
checkm	scipy 1.5.4 is only compatible with python 3.6+	2020-12-24 09:03:39 +00:00
clustal-omega
clustalw
cufflinks	- Upgrade math/eigen3 to 3.3.8;	2020-12-12 17:04:37 +00:00
cytoscape
ddocent
diamond	biology/diamond: Update to version 2.0.6	2020-12-20 20:21:41 +00:00
dsr-pdb
edlib	Fix build on GCC-based systems by adding compiler:c++14-lang to USES:	2021-01-20 02:31:33 +00:00
emboss
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastp
fastqc	biology/fastqc: Update to 0.11.9	2021-02-04 15:56:33 +00:00
fasttree	biology/fasttree: Drop dependency on gcc	2021-01-11 16:58:13 +00:00
fastx-toolkit
figtree	Add education virtual category	2020-11-20 07:16:06 +00:00
fluctuate
freebayes	For ports on riscv64 that fail the same (or similar ways) to aarch64, mark	2021-01-02 01:46:08 +00:00
garlic
gatk	biology/gatk: Add the WITH_LARGE_FILES option.	2021-01-22 02:50:38 +00:00
gcta	biology/gcta: Drop dependency on gcc	2021-01-11 17:09:37 +00:00
gemma	biology/gemma: Upgrade to 0.98.3	2021-01-02 22:05:58 +00:00
gff2ps
gmap	biology/gmap: enable on powerpc64le	2020-10-09 13:23:12 +00:00
gperiodic
graphlan
grappa
groopm	scipy 1.5.4 is only compatible with python 3.6+	2020-12-24 09:03:39 +00:00
haplohseq	biology/haplohseq: Fix example scripts for python 3	2021-01-23 19:31:49 +00:00
hhsuite
hisat2
hmmer	Also enable on powerpc64le.	2020-09-24 20:29:35 +00:00
htslib	biology/htslib: Upgrade to 1.11.0	2020-11-05 20:30:50 +00:00
hyphy	biology/hyphy: Update to version 2.5.27	2021-01-27 11:33:53 +00:00
igv	biology/igv: Fix fetch by fixing a small left-over mistake	2020-11-30 17:29:48 +00:00
infernal	Also enable on powerpc64le.	2020-09-24 20:38:59 +00:00
iolib
iqtree	biology/iqtree: Remove USES=compiler:openmp, fix amd64 clang++ build	2021-01-12 18:12:12 +00:00
jalview	Restrict to Java 8, since this doesn't compile with Java 11	2020-12-26 23:01:20 +00:00
jellyfish
kallisto	biology/kallisto: Add -lz for pending hdf5 upgrade	2021-01-26 01:34:20 +00:00
lagan
lamarc
libbigwig
libgtextutils
libsbml	Set CMAKE options explicitly	2020-12-20 15:23:50 +00:00
linux-foldingathome
mafft
mapm3
migrate	Mark BROKEN on riscv64 the same as armv*:	2021-01-19 02:26:53 +00:00
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+	biology/ncbi-blast+: Drop dependency on gcc	2021-01-11 17:17:35 +00:00
ncbi-cxx-toolkit	biology/ncbi-cxx-toolkit: Fix build on 13	2020-09-27 04:57:44 +00:00
ncbi-toolkit
ngs-sdk	For ports on riscv64 that fail the same (or similar ways) to aarch64, mark	2021-01-02 01:46:08 +00:00
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
pbbam
pbseqan
pear-merger	For ports on riscv64 that fail the same (or similar ways) to aarch64, mark	2021-01-02 01:46:08 +00:00
phrap
phred
phylip
phyml
picard-tools
plink	Allow building on powerpc64le.	2020-09-27 07:44:15 +00:00
pooler	biology/pooler: Upgrade to 1.76	2021-01-08 22:44:13 +00:00
primer3
prodigal
prodigy-lig
protomol
psi88
py-biom-format	Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+	2021-01-30 13:29:58 +00:00
py-biopython	biology/py-biopython: Upgrade to 1.78	2020-10-16 19:12:43 +00:00
py-bx-python	Drop python 2.7 support from a few ports	2020-12-28 23:02:12 +00:00
py-cutadapt	biology/py-cutadapt: Update to 3.2	2021-02-02 20:39:09 +00:00
py-dnaio	biology/py-cutadapt: Update to 3.2	2021-02-02 20:39:09 +00:00
py-ete3	Update PyQt5 to 5.15.2, sip to 5.5.0, py-qtbuilder to 1.6.0 and py-qt5-sip to 12.8.1	2020-12-15 17:56:00 +00:00
py-fastTSNE
py-Genesis-PyAPI	Drop python 2.7 support from a few ports	2020-12-28 23:02:12 +00:00
py-gffutils
py-gtfparse	Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+	2021-01-30 13:29:58 +00:00
py-hits
py-loompy	Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+	2021-01-30 13:29:58 +00:00
py-macs2
py-multiqc	biology/py-multiqc: Update to 1.9	2021-02-05 01:37:04 +00:00
py-orange3-bioinformatics
py-orange3-single-cell	Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+	2021-01-30 13:29:58 +00:00
py-pandas-charm	Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+	2021-01-30 13:29:58 +00:00
py-pyfaidx	Drop python 2.7 support from a few ports	2020-12-28 23:02:12 +00:00
py-pysam	Drop python 2.7 support from a few ports	2020-12-28 23:02:12 +00:00
py-scikit-bio	Add education virtual category	2020-11-20 07:16:06 +00:00
py-xenaPython	Drop python 2.7 support from a few ports	2020-12-28 23:02:12 +00:00
pyfasta	Drop python 2.7 support from a few ports	2020-12-28 23:02:12 +00:00
python-nexus	Drop python 2.7 support from a few ports	2020-12-28 23:02:12 +00:00
rainbow
rampler	Add compiler:c++11-lang to USES to fix build on GCC-based systems:	2021-01-20 02:30:13 +00:00
recombine
ruby-bio
rubygem-bio
rubygem-bio-executables
rubygem-bio-old-biofetch-emulator
rubygem-bio-shell
samtools	biology/samtools: Upgrade to 1.11	2020-11-05 20:32:39 +00:00
scrm
seaview
seqan
seqan1
seqan-apps
seqio
seqtk
sim4
slclust
smithwaterman
spoa	New port: biology/spoa: C++ implementation of the partial order alignment (POA) algorithm	2021-01-19 09:28:00 +00:00
stacks	biology/stacks: Drop dependency on gcc	2021-01-11 17:27:30 +00:00
star	biology/star: Drop dependency on gcc	2021-01-11 17:39:52 +00:00
stringtie
subread
tabixpp	biology/tabixpp: fix build on GCC architectures	2020-11-23 16:13:15 +00:00
treekin
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ugene	Mark BROKEN on riscv64 the same as on aarch64.	2021-01-19 02:29:16 +00:00
vcflib	For ports on riscv64 that fail the same (or similar ways) to aarch64, mark	2021-01-02 01:46:08 +00:00
vcftools
velvet
viennarna	biology/viennarna: Update 2.4.16 -> 2.4.17	2020-12-06 20:14:53 +00:00
vsearch	biology/vsearch: Update to 2.15.2	2021-01-30 15:31:11 +00:00
vt	biology/vt: Fix build with htslib 1.11	2020-11-09 00:35:58 +00:00
wise
Makefile	New port: biology/rampler: Standalone module for sampling genomic sequences	2021-01-19 09:49:53 +00:00