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freebsd-ports/biology
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Fernando Apesteguía 07fb2d5e9d */*: Remove compiler:openmp from Mk/Uses/compiler.mk 
The option implied a dependency on gcc but clang got openmp support long ago.

Remove compiler:openmp from Mk/Uses/compiler.mk

For ports using USE=compiler:openmp, just remove it and make them build with
clang.
Fix conditionals when necessary
Bump PORTREVISION where appropriate

If problem arises, they can be addressed by using USE_GCC=yes

An update to the Porter's Handbook will follow.

Approved by: portmgr (bapt)
Differential Revision: https://reviews.freebsd.org/D31971
2021-10-03 19:47:27 +02:00
..
abyss cleanup: drop support for EOL FreeBSD 11.X 2021-09-30 23:23:30 +02:00
ad2vcf biology/ad2vcf: Update to 0.1.3.31 2021-08-27 20:28:10 -05:00
artemis Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
avida Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
babel all: Remove all other $FreeBSD keywords. 2021-04-06 16:31:13 +02:00
bamtools biology/bamtools: Update to 2.5.2 2021-07-06 13:10:54 -05:00
bbmap biology/bbmap: Update to 38.92 2021-08-22 08:59:58 -05:00
bcftools biology/bcftools: Update to 1.13 2021-07-12 08:30:10 -05:00
bedtools One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
bfc biology/bfc: Correct sequencing errors from Illumina sequencing data 2021-08-23 12:28:41 -05:00
bioawk One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
biococoa One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
biolibc biology/biolibc: Update to 0.2.0.11 2021-09-17 11:33:57 -05:00
biolibc-tools biology/biolibc-tools: High-performance tools based on biolibc 2021-08-30 08:09:23 -05:00
bioparser biology/bioparser: Update 3.0.12-2 -> 3.0.15 2021-09-21 09:41:49 -07:00
biosig biology/biosig: Add DISTNAME instead of DISTVERSIONSUFFIX 2021-08-16 19:57:30 -07:00
biosoup One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
biostar-tools biology/biostar-tools: Add biology/kallisto run depend to metaport 2021-09-27 07:14:45 -05:00
bolt-lmm One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
bowtie One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
bowtie2 biology/bowtie2: Update to 2.4.4 2021-05-24 11:35:43 -05:00
bwa One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
canu One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
cd-hit biology/cd-hit: fix build on powerpc 2021-06-10 00:35:36 +00:00
cdbfasta Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
checkm math/py-matplotlib: chase minimum Python version in dependent ports 2021-05-10 22:13:20 +02:00
clustal-omega One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
clustalw Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
cufflinks One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
cytoscape biology/cytoscape: mark unconditionally BROKEN 2021-05-12 14:55:52 +03:00
ddocent cleanup: drop support for EOL FreeBSD 11.X 2021-09-30 23:23:30 +02:00
diamond biology/diamond: Update to 2.0.11-1 2021-07-06 10:15:24 -03:00
dsr-pdb One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
edlib biology/edlib: Update 1.2.6.20201202 -> 1.2.7 2021-08-21 10:12:15 -07:00
emboss biology/emboss: Add "emboss" command in ${LOCALBASE}/bin 2021-09-24 16:34:20 -05:00
erminej biology/erminej: Analyses of gene sets, e.g. gene expression profiling 2021-07-09 07:26:58 -05:00
exonerate Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
fasta Deorbit RESTRICTED && NO_CDROM, part two. 2021-05-06 13:47:48 +02:00
fasta3 Deorbit RESTRICTED && NO_CDROM, part one. 2021-05-06 13:47:41 +02:00
fastahack One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
fastdnaml Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
fastool One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
fastp biology/fastp: Update to 0.22.0 2021-08-26 14:48:10 -05:00
fastqc One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
fasttree biology/fasttree: fix build on armv7 2021-06-15 08:41:19 +00:00
fastx-toolkit One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
figtree One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
flash biology/flash: Fast Length Adjustment of SHort reads 2021-08-23 12:26:47 -05:00
fluctuate Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
freebayes One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
garlic Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
gatk One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
gcta One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
gemma math/gsl: update to 2.7 2021-06-16 21:31:27 +02:00
generand One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
gff2ps Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
gmap Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
gperiodic Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
graphlan One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
groopm math/py-matplotlib: chase minimum Python version in dependent ports 2021-05-10 22:13:20 +02:00
haplohseq One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
hhsuite biology/hhsuite: Fix build on aarch64 2021-09-13 17:47:57 +02:00
hisat2 One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
hmmer Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
htslib biology/htslib: Add CPE information 2021-09-10 21:18:20 +00:00
hyphy biology/hyphy: Update to 2.4.32 2021-08-20 10:56:52 -03:00
igv cleanup: drop support for EOL FreeBSD 11.X 2021-09-30 23:23:30 +02:00
infernal One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
iolib biology/iolib: Drop maintainership 2021-05-19 20:56:24 +01:00
iqtree One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
jalview cleanup: drop support for EOL FreeBSD 11.X 2021-09-30 23:23:30 +02:00
jellyfish biology/jellyfish: Switch to static tarball and update license info 2021-09-17 15:01:35 -03:00
kallisto One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
lamarc Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
libbigwig One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
libgtextutils One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
libnuml biology/libnuml: New port: C++ library for Numerical Markup Language 2021-09-18 23:47:02 -07:00
libsbml biology/libsbml: Rename LIBXML option to LIBXML2 2021-05-12 05:46:56 +08:00
libsedml biology/libsedml: New port: C++ SED-ML library 2021-09-19 11:15:35 -07:00
linux-foldingathome biology/linux-foldingathome: Update to 7.6.21 2021-06-25 19:13:19 +02:00
mafft Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
mapm3 Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
migrate Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
minimap2 biology/minimap2: Add pkg-plist to repo 2021-08-22 12:46:37 -05:00
mmseqs2 biology/mmseqs2: disable on 32-bits 2021-09-12 21:05:53 +00:00
molden graphics/mesa-libs: Bump reverse deps for libglvnd 2021-06-22 11:53:08 -07:00
mopac Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
mothur biology/mothur: Update 1.46.0 -> 1.46.1 2021-09-02 02:29:56 -07:00
mrbayes *: Remove unnecessary 'port' argument from USES=readline 2021-05-15 09:14:04 +02:00
mummer Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
muscle Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
ncbi-blast+ biology/ncbi-blast+: Update to 2.12.0 2021-07-02 11:48:20 -05:00
ncbi-cxx-toolkit biology/ncbi-cxx-toolkit: Update 25.0.0 -> 25.2.0 2021-10-01 00:14:37 -07:00
ncbi-entrez-direct biology/ncbi-entrez-direct: Update to 14.9.20210423_1 2021-04-26 11:53:11 -05:00
ncbi-toolkit Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
ncbi-vdb devel/libepoll-shim: update to 0.0.20210418 2021-04-26 14:17:32 +00:00
ngs-sdk biology/ngs-sdk: Update 2.11.0-> 2.11.1 2021-08-18 10:17:44 -07:00
p5-AcePerl Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-ASN1-EntrezGene Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Cluster Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Coordinate Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Das Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Das-Lite Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-DB-EMBL Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-DB-NCBIHelper biology/p5-Bio-DB-NCBIHelper: Update to 1.7.7 2021-07-06 22:56:10 +08:00
p5-Bio-FeatureIO Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-GFF3 Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Glite Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Graphics Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-MAGETAB Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-NEXUS Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Phylo Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-SCF Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-Bio-Variation Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-BioPerl Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-BioPerl-Run Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
p5-transdecoder One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
p5-TrimGalore One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
paml Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
pbbam One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
pbseqan One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
peak-classifier biology/peak-classifier: Update to 0.1.1.21 2021-09-02 18:15:40 -05:00
pear-merger One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
phrap Deorbit RESTRICTED && NO_CDROM, part two. 2021-05-06 13:47:48 +02:00
phred Deorbit RESTRICTED && NO_CDROM, part two. 2021-05-06 13:47:48 +02:00
phyml Clean up some things 2021-04-15 10:31:56 +02:00
picard-tools One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
plink One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
pooler */*: Remove compiler:openmp from Mk/Uses/compiler.mk 2021-10-03 19:47:27 +02:00
primer3 Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
prodigal One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
prodigy-lig One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
protomol Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
psi88 Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
py-bigwig biology/py-bigwig: Fix packaging with Python 3.8+ 2021-04-21 09:41:29 +02:00
py-biom-format One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-biopython Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
py-bx-python biology/py-bx-python: Update 0.8.10 -> 0.8.11-6 2021-08-17 12:10:45 -07:00
py-crossmap biology/py-crossmap: Update to 0.5.4 2021-04-21 08:31:13 -05:00
py-cutadapt biology/py-cutadapt: Update strict py-dnaio dep version 2021-05-04 08:20:39 -05:00
py-dnaio biology/py-dnaio: Update to 0.5.1 2021-05-04 08:19:25 -05:00
py-ete3 One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-Genesis-PyAPI One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-gffutils One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-goatools biology/py-goatools: Tools for processing and visualizing Gene Ontology terms 2021-07-02 12:00:29 -05:00
py-gtfparse One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-hits One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-libnuml biology/py-libnuml: Fix typo 2021-09-19 11:15:35 -07:00
py-libsedml biology/py-libsedml: New port: SED-ML library for Python 2021-09-19 11:15:36 -07:00
py-loompy One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-macs2 One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-multiqc math/py-matplotlib: chase minimum Python version in dependent ports 2021-05-10 22:13:20 +02:00
py-ont-fast5-api biology/py-ont-fast5-api: Interface to Oxford Nanopore .fast5 files 2021-08-13 08:34:09 -05:00
py-orange3-bioinformatics biology/py-orange3-bioinformatics: Update 3.2.2 -> 4.3.1 2021-04-27 01:56:19 -07:00
py-orange3-single-cell One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-pandas-charm One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-pyfaidx biology/py-pyfaid: Update 0.5.9.2 -> 0.5.9.5 2021-04-23 14:57:50 -07:00
py-pysam One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-PySCeS biology/py-PySCeS: Update 0.9.8a -> 1.0.0 2021-09-20 14:34:22 -07:00
py-python-libsbml biology/py-python-libsbml: New port: LibSBML Python API 2021-08-17 14:30:07 -07:00
py-pywgsim biology/py-pywgsim: Modified wgsim genomic data simulator 2021-09-06 07:55:49 -05:00
py-resdk biology/py-resdk: Update 13.3.0 -> 13.4.0 2021-08-17 10:29:42 -07:00
py-scikit-bio One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-xenaPython One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
pyfasta Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
python-nexus Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
rainbow One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
rampler One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
readseq biology/readseq: Remove $FreeBSD$ tag inserted to silence portlint 2021-04-18 09:20:28 -05:00
recombine Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
ruby-bio Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
rubygem-bio biology/rubygem-bio: Update to 2.0.2 2021-07-01 04:44:06 +08:00
rubygem-bio-executables Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
rubygem-bio-old-biofetch-emulator Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
rubygem-bio-shell Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
sam2pairwise biology/sam2pairwise: Show pairwise alignment for each read in a SAM file 2021-09-07 15:32:29 -05:00
samtools biology/samtools: Update to 1.13 2021-07-12 08:24:26 -05:00
scrm One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
seaview biology/seaview: in preparation to FLTK update, unbreak the port 2021-08-14 08:58:03 +00:00
seqan Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
seqan1 Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
seqan3 biology/seqan3: Add the 'test' target (currently broken due to lacking clang support) 2021-08-13 10:08:56 -07:00
seqan-apps */*: Remove compiler:openmp from Mk/Uses/compiler.mk 2021-10-03 19:47:27 +02:00
seqio Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
seqkit biology/seqkit: Update 0.16.1 -> 2.0.1 2021-09-18 10:48:26 -07:00
seqtk One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
sigviewer misc/: Update 0.99.6-2 -> 0.991 2021-08-18 10:17:45 -07:00
sim4 Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
slclust One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
smithwaterman One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
snpeff biology/snpeff: Improvements to Makefile and patches 2021-04-19 11:41:58 -05:00
spoa One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
sra-tools biology/sra-tools: NCBI's toolkit for handling data in INSDC Sequence Read Archives 2021-06-22 12:55:15 -05:00
stacks One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
star One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
stringtie One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
subread One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
tabixpp One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
taxonkit biology/taxonkit: New port: Practical and efficient NCBI taxonomy toolkit 2021-05-26 15:25:22 -07:00
treekin math/lapack: +math/blas et al., upgrade to 3.9.1 2021-06-13 19:48:12 +02:00
treepuzzle Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
trimadap One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
trimmomatic Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
tRNAscan-SE Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
ucsc-userapps biology/ucsc-userapps: Add "kent" command in ${PREFIX}/bin 2021-09-24 16:53:30 -05:00
ugene biology/ugene: update Unipro UGENE to version 40.0. 2021-09-16 09:48:26 +00:00
unikmer biology/unikmer: Update 0.18.4 -> 0.18.8 2021-09-26 01:54:07 -07:00
vcf2hap biology/vcf2hap: Update to 0.1.3.12 2021-08-27 20:32:51 -05:00
vcf-split biology/vcf-split: Update to 0.1.2.14 2021-08-27 20:30:52 -05:00
vcflib One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
vcftools biology/vcftools: Add CPE information 2021-09-25 20:28:38 +00:00
velvet Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
viennarna math/gsl: update to 2.7 2021-06-16 21:31:27 +02:00
vsearch biology/vsearch: Update to 2.17.1 2021-06-19 07:33:58 -05:00
vt One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
wise Remove # $FreeBSD$ from Makefiles. 2021-04-06 16:31:07 +02:00
Makefile */Makefile: Sort SUBDIRs 2021-09-21 11:35:06 +08:00