Joseph Mingrone 56dac58885 biology/hyphy: Remove USES=compiler:openmp ... USES=compiler:openmp still forces building with GCC. This is no longer necessary on tier 1 platforms, which have openmp in the base system. PR: 247753, 252379		2021-01-11 17:54:42 +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	Bump devel/jsoncpp consumers after r540853.	2020-06-30 17:46:18 +00:00
bcftools	biology/bcftools: Upgrade to 1.11	2020-11-05 20:34:03 +00:00
bedtools
bioawk	biology/bioawk: BWK awk modified for biological data	2020-06-05 02:45:33 +00:00
biococoa
bolt-lmm	Canonicalize powerpc64le CXXFLAGS to be the same as powerpc64.	2020-09-27 07:41:33 +00:00
bowtie	biology/bowtie: Unbreak build with GCC 10	2020-07-04 10:46:08 +00:00
bowtie2	biology/bowtie2: Upgrade to 2.4.2	2020-11-07 13:47:41 +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
emboss	- update libgd to 2.3.0	2020-05-04 21:31:39 +00:00
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastp	biology/fastp: Upgrade to 0.20.1	2020-04-09 16:17:02 +00:00
fastqc
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: Fix build	2020-09-08 19:25:36 +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	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	scipy 1.5.4 is only compatible with python 3.6+	2020-12-24 09:03:39 +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	biology/htslib: Upgrade to 1.11.0	2020-11-05 20:30:50 +00:00
hyphy	biology/hyphy: Remove USES=compiler:openmp	2021-01-11 17:54:42 +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	- Upgrade math/eigen3 to 3.3.8;	2020-12-12 17:04:37 +00:00
jalview	Restrict to Java 8, since this doesn't compile with Java 11	2020-12-26 23:01:20 +00:00
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	Extend expiration of ports broken with -fno-common	2020-08-30 09:47:49 +00:00
lamarc
libbigwig
libgtextutils
libsbml	Set CMAKE options explicitly	2020-12-20 15:23:50 +00:00
linux-foldingathome	Update to 7.6.13	2020-05-09 13:21:29 +00:00
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	- Swap back from net/openmpi3 to net/openmpi	2020-04-21 21:47:57 +00:00
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	Chase security/p11-kit update	2020-08-30 03:10:23 +00:00
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	Cosmetic change	2020-04-02 12:01:30 +00:00
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-DB-EMBL
p5-Bio-DB-NCBIHelper
p5-Bio-FeatureIO	Cosmetic change	2020-04-02 12:01:35 +00:00
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	For ports on riscv64 that fail the same (or similar ways) to aarch64, mark	2021-01-02 01:46:08 +00:00
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	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
pooler	biology/pooler: Upgrade to 1.76	2021-01-08 22:44:13 +00:00
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-biom-format	biology/py-biom-format: Update to version 2.1.10	2021-01-11 05:28:11 +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
py-dnaio	biology/py-dnaio: Upgrade to 0.4.2	2020-05-24 15:23:15 +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	Unbreak bulk -a	2020-07-14 07:59:28 +00:00
py-gtfparse	Drop python 2.7 support from a few ports	2020-12-28 23:02:12 +00:00
py-hits	New port: biology/py-hits: Utilities for processing high-throughput sequencing experiments	2020-05-16 03:11:05 +00:00
py-loompy	biology/py-loompy: Update 2.0.17 -> 3.0.6	2020-06-16 02:26:08 +00:00
py-macs2	biology/py-macs2: Upgrade to 2.2.7.1	2020-04-14 12:13:55 +00:00
py-multiqc	Unbreak bulk -a	2020-09-19 14:15:42 +00:00
py-orange3-bioinformatics
py-orange3-single-cell	Update Sphinx	2020-05-11 23:51:58 +00:00
py-pandas-charm	Drop python 2.7 support from a few ports	2020-12-28 23:02:12 +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	Update WWW	2020-03-31 23:18:09 +00:00
recombine
ruby-bio	biology/ruby-bio: remove expired optional dependency on textproc/ruby-xmlparser	2020-05-05 14:22:09 +00:00
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 1.11	2020-11-05 20:32:39 +00:00
scrm	Add compiler:c++11-lang to USES to fix build on GCC-based systems:	2020-05-15 07:30:34 +00:00
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	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	biology/subread: Add -fcommon for clang 11	2020-09-18 00:57:35 +00:00
tabixpp	biology/tabixpp: fix build on GCC architectures	2020-11-23 16:13:15 +00:00
treekin
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ugene	- Update Unipro UGENE port to version 37.0	2020-12-31 13:43:09 +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 2.15.0	2020-06-20 14:31:59 +00:00
vt	biology/vt: Fix build with htslib 1.11	2020-11-09 00:35:58 +00:00
wise
Makefile	biology/pooler: Optimise DNA sequencing primer-set combinations	2020-11-15 18:50:17 +00:00