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freebsd-ports/biology
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Fernando Apesteguía 8d34513c3f biology/pooler: update to 1.82 
ChangeLog: http://ssb22.user.srcf.net/pooler/#changes

PR:	261741
Reported by:	silas-freebsd@flatline.org.uk
2022-02-10 15:23:48 +01:00
..
abyss cleanup: drop support for EOL FreeBSD 11.X 2021-09-30 23:23:30 +02:00
ad2vcf biology/ad2vcf: Update to 0.1.4 2021-12-14 13:45:31 -06:00
artemis
avida
babel */*: Remove redundant '-*' from CONFLICTS definitions 2021-11-25 22:40:11 +01:00
bamtools devel/jsoncpp: Update to 1.9.4 -> 1.9.5 2021-11-05 12:09:19 -07:00
bamutil Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
bbmap biology/bbmap: Update to 38.92 2021-08-22 08:59:58 -05:00
bcftools math/gsl: bump portrevision of consumers after update to 2.7.1 2022-01-12 20:41:22 +01:00
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
bio-mocha biology/bio-mocha: Update to 1.14-20220112 2022-01-13 13:00:41 -06:00
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 0.2.1 2021-12-14 13:45:31 -06:00
biolibc-tools biology/biolibc-tools: Update to 0.1.1 2021-12-14 13:45:32 -06:00
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: Allow package build on non-amd64 systems 2021-12-01 09:49:28 -06:00
bolt-lmm Update CONFLICTS definitions in categories a* to c* 2022-02-06 19:36:07 +01:00
bowtie biology/bowtie: enable on riscv64 2021-12-15 13:55:57 +01:00
bowtie2 biology/bowtie2: Update to 2.4.5 2022-01-21 08:33:54 -06:00
bwa biology/bwa: don't use GCC on powerpc64le 2021-12-01 17:34:18 +00:00
canu biology/canu: fix CATEGORIES 2021-12-20 12:59:13 +00:00
cd-hit biology/cd-hit: fix build on armv7 2021-11-21 13:26:44 +00:00
cdbfasta
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
cufflinks Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
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 2.0.14 2022-01-13 13:42:38 -04:00
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 */*: Remove redundant '-[0-9]*' from CONFLICTS 2021-10-29 11:50:18 +02:00
erminej biology/erminej: Analyses of gene sets, e.g. gene expression profiling 2021-07-09 07:26:58 -05:00
exonerate
fasta Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
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
fastool One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
fastp biology/fastp: Add USE_GCC to hack around seg faults 2022-01-21 10:16:01 -06:00
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 Update CONFLICTS definitions in categories a* to c* 2022-02-06 19:36:07 +01:00
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
freebayes biology/freebayes: Update to 1.3.6 2022-02-06 14:23:45 -06:00
garlic
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: bump portrevision of consumers after update to 2.7.1 2022-01-12 20:41:22 +01:00
generand One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
gff2ps
gffread Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
gmap Update CONFLICTS definitions in categories a* to c* 2022-02-06 19:36:07 +01:00
gperiodic
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 packaging on powerpc 2021-11-16 12:03:42 +00:00
hisat2 biology/hisat2: enable on riscv64 2021-12-16 22:38:56 +01:00
hmmer
htslib biology/htslib: Update to 1.14 2021-12-18 11:56:50 -06:00
hyphy biology/hyphy: Update to 2.5.36 2022-02-03 01:42:15 -04:00
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 Update CONFLICTS definitions in categories a* to c* 2022-02-06 19:36:07 +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 *: Clean up some things 2021-10-12 17:01:38 +02:00
kallisto biology/kallisto: Update to 0.48.0 2022-01-19 07:57:36 -06:00
lamarc
libbigwig One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
libgff biology/libgff: GFF/GTF parsing library based on GCLib 2021-12-05 14:50:42 -06:00
libgtextutils One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
libneurosim biology/libneurosim: New port: Common interfaces for neuronal simulators 2021-10-08 10:20:27 -07:00
libnuml biology/libnuml: New port: C++ library for Numerical Markup Language 2021-09-18 23:47:02 -07:00
libsbml biology/libsbml: Fix build with Python 3.10 2021-11-02 05:28:40 +08:00
libsedml biology/libsedml: New port: C++ SED-ML library 2021-09-19 11:15:35 -07:00
linux-foldingathome Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.) 2021-10-25 12:58:29 +00:00
mafft biology/mafft: Update to 7.267 2021-10-22 13:11:23 +08:00
mapm3
migrate Update CONFLICTS definitions in categories a* to c* 2022-02-06 19:36:07 +01:00
minimap2 biology/minimap2: Update to 2.24 2021-12-31 08:30:52 -06:00
mmseqs2 biology/mmseqs2: disable on 32-bits 2021-09-12 21:05:53 +00:00
molden *: Clean up some things 2022-01-17 14:20:25 +01:00
mopac
mothur biology/mothur: Update 1.46.1 -> 1.47.0 2022-01-21 09:14:38 -08:00
mrbayes *: Remove unnecessary 'port' argument from USES=readline 2021-05-15 09:14:04 +02:00
mummer Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
muscle
ncbi-blast+ biology/ncbi-blast+: fix build on powerpc 2022-01-22 13:33:19 +00:00
ncbi-cxx-toolkit Update CONFLICTS definitions in categories a* to c* 2022-02-06 19:36:07 +01:00
ncbi-entrez-direct Update CONFLICTS definitions in categories a* to c* 2022-02-06 19:36:07 +01:00
ncbi-toolkit Update CONFLICTS definitions in categories a* to c* 2022-02-06 19:36:07 +01:00
ncbi-vdb security/mbedtls: Update to 2.28.0 and fix make test 2022-01-28 13:14:09 +01:00
ngs-sdk biology/ngs-sdk: Update 2.11.1 -> 2.11.2 2022-01-27 01:29:09 -08:00
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 biology/p5-Bio-DB-NCBIHelper: Update to 1.7.7 2021-07-06 22:56:10 +08:00
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 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
pbbam *: fix tab vs. space issues, and comments according to the guide. 2021-10-16 11:51:39 +02:00
pbseqan *: fix tab vs. space issues, and comments according to the guide. 2021-10-16 11:51:39 +02:00
peak-classifier biology/peak-classifier: Update to 0.1.2 2021-12-14 13:45:32 -06:00
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 biology/phyml: update to 3.3.20211231 2022-01-02 18:31:24 +01:00
picard-tools Update CONFLICTS definitions in categories a* to c* 2022-02-06 19:36:07 +01:00
plink Update CONFLICTS definitions in categories a* to c* 2022-02-06 19:36:07 +01:00
pooler biology/pooler: update to 1.82 2022-02-10 15:23:48 +01:00
primer3
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
psi88
py-bcbio-gff biology/py-bcbio-gff: Read and write Generic Feature Format (GFF) 2022-02-03 13:38:42 -06:00
py-biom-format One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-biopython biology/py-biopython: Update to 1.79 2021-10-12 14:43:04 +08:00
py-bx-python biology/py-bx-python: Update 0.8.11-6 -> 0.8.13 2021-12-21 01:03:57 -08:00
py-crossmap biology/py-crossmap: chase ad5a0604c4 2021-10-14 00:53:16 +00:00
py-cutadapt biology/py-cutadapt: Update strict py-dnaio dep version 2021-05-04 08:20:39 -05:00
py-deeptools biology/py-deeptools: User-friendly tools for exploring deep-sequencing data 2021-10-14 06:51:12 -05:00
py-deeptoolsintervals biology/py-deeptoolsintervals: Python interface for deepTools interval trees 2021-10-13 11:02:13 -05:00
py-dna-features-viewer biology/py-dna-features-viewer: Add py-bcbio-gff dep 2022-02-03 14:11:38 -06:00
py-dnaio biology/py-dnaio: Update to 0.5.1 2021-05-04 08:19:25 -05:00
py-ete3 PyQt: Update sip to 6.5.0, reintroduce sip4 and simplify PyQt framework. 2022-01-27 07:12:26 +01:00
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 install with python 3.10+ 2021-11-02 21:08:32 +03:00
py-libsedml biology/py-libsedml: fix install with python 3.10+ 2021-11-02 21:08:31 +03:00
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 cleanup: remove transitive py27 deprecation (www/qt5-webengine) 2022-01-23 21:56:25 +01:00
py-orange3-single-cell cleanup: remove transitive py27 deprecation (www/qt5-webengine) 2022-01-23 21:56:25 +01:00
py-pandas-charm One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
py-py2bit biology/py-py2bit: Python interface for 2bit packed nucleotide files 2021-10-13 07:53:53 -05:00
py-pybigwig biology/py-bigwig: Rename to biology/py-pybigwig 2021-10-13 16:21:32 -05:00
py-pyfaidx biology/py-pyfaid: Update 0.5.9.2 -> 0.5.9.5 2021-04-23 14:57:50 -07:00
py-pysam biology/py-pysam: Update 0.16.0.1 -> 0.18.0 2021-12-19 23:48:52 -08:00
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: limit supported python versions, fix build 2021-11-03 21:26:41 +03:00
py-pywgsim biology/py-pywgsim: Modified wgsim genomic data simulator 2021-09-06 07:55:49 -05:00
py-resdk biology/py-resdk: Update 13.8.0 -> 14.0.0 2022-01-19 10:10:01 -08:00
py-scikit-bio Update CONFLICTS definitions in categories a* to c* 2022-02-06 19:36:07 +01:00
py-xenaPython One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
pyfasta
python-nexus
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
ruby-bio Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
rubygem-bio biology/rubygem-bio: Update to 2.0.3 2022-01-12 02:47:28 +08:00
rubygem-bio-executables
rubygem-bio-old-biofetch-emulator
rubygem-bio-shell Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
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 1.14 2021-12-18 11:56:51 -06:00
scrm One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
seaview biology/seaview: Update version 5.0.4=>5.0.5 2021-12-05 19:02:42 -06:00
seqan */*: Remove redundant '-[0-9]*' from CONFLICTS 2021-10-29 11:50:18 +02:00
seqan1 Update CONFLICTS definitions in categories a* to c* 2022-02-06 19:36:07 +01:00
seqan3 biology/seqan3: Update 3.0.3 -> 3.1.0 2021-11-14 21:18:53 -08:00
seqan-apps */*: Remove compiler:openmp from Mk/Uses/compiler.mk 2021-10-03 19:47:27 +02:00
seqio
seqkit biology/seqkit: Update 2.0.1 -> 2.1.0 2021-11-16 10:57:47 -08:00
seqtk biology/seqtk: Update to 1.3 2021-12-18 13:37:06 -06:00
sigviewer misc/: Update 0.99.6-2 -> 0.991 2021-08-18 10:17:45 -07:00
sim4
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 devel/cpu_features: Install cmake files, install headers into a dedicated directory 2022-01-26 08:45:29 -08:00
sra-tools Fix CONFLICTS entries of multiple ports 2022-01-10 16:15:39 +01:00
stacks One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
star biology/star: Update to 2.7.9a 2021-11-26 15:57:02 -06:00
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: Update 0.8.0 -> 0.9.0 2021-12-02 12:57:06 -08:00
treekin biology/treekin: Unbreak 2021-10-15 08:50:24 -07:00
treepuzzle
trimadap Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.) 2021-10-25 12:58:29 +00:00
trimmomatic
tRNAscan-SE
ucsc-userapps Style: improve ONLY_FOR_ARCHS_REASON (grammar, markup, etc.) 2021-10-25 12:58:29 +00:00
ugene biology/ugene: update UniPro UGENE to version 40.1 (bugfix release). 2021-10-14 11:23:37 +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 0.1.4 2021-12-14 13:45:32 -06:00
vcf-split biology/vcf-split: Update to 0.1.3.3 2021-12-14 13:45:32 -06:00
vcflib Update CONFLICTS definitions in categories a* to c* 2022-02-06 19:36:07 +01:00
vcftools biology/vcftools: Add CPE information 2021-09-25 20:28:38 +00:00
velvet
viennarna Update CONFLICTS definitions in categories a* to c* 2022-02-06 19:36:07 +01:00
vsearch biology/vsearch: Update to 2.21.1 2022-01-23 16:32:43 -06:00
vt One more small cleanup, forgotten yesterday. 2021-04-07 10:09:01 +02:00
wise
Makefile biology/py-bcbio-gff: Read and write Generic Feature Format (GFF) 2022-02-03 13:38:42 -06:00