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freebsd-ports/biology
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Jason W. Bacon 2394925fbc biology/ncbi-blast+: Upgrade to 2.11.0 
A few bug fixes and performance improvements since 2.10.0
Also overcomes GCC 10 build issues

PR:             ports/246700
Reported by:    linimon
2020-11-16 18:25:03 +00:00
..
abyss
biology/abyss: Update 2.2.4 -> 2.2.5
2020-09-27 06:59:05 +00:00
artemis
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avida
…
babel
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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
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bioawk
biology/bioawk: BWK awk modified for biological data
2020-06-05 02:45:33 +00:00
biococoa
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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
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
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cdbfasta
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checkm
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clustal-omega
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clustalw
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cufflinks
biology/cufflinks: fix build on recent current
2020-08-28 18:24:04 +00:00
cytoscape
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ddocent
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diamond
biology/diamond: Update to version 2.0.4
2020-08-30 16:14:22 +00:00
dsr-pdb
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emboss
- update libgd to 2.3.0
2020-05-04 21:31:39 +00:00
exonerate
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fasta
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fasta3
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fastahack
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fastdnaml
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fastool
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fastp
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fastqc
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fasttree
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fastx-toolkit
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figtree
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fluctuate
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freebayes
Fix build with -fno-common
2020-09-21 18:14:57 +00:00
garlic
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gatk
biology/gatk: Fix build
2020-09-08 19:25:36 +00:00
gcta
biology/gcta: Switch eigen3 dep to USES framework
2020-11-08 14:31:00 +00:00
gemma
Bump 37 ports depending on math/openblas through USES=blaslapack:openblas because after the recent math/openblas update the library name changed in openblas
2020-05-06 16:39:12 +00:00
gff2ps
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gmap
biology/gmap: enable on powerpc64le
2020-10-09 13:23:12 +00:00
gperiodic
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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
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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 2.5.21
2020-10-30 14:05:47 +00:00
igv
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infernal
Also enable on powerpc64le.
2020-09-24 20:38:59 +00:00
iolib
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iqtree
biology/iqtree: Update to version 2.0.6
2020-05-30 18:43:26 +00:00
jalview
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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
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libbigwig
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libgtextutils
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libsbml
Convert REINPLACE_CMD to patch file
2020-09-29 18:23:04 +00:00
linux-foldingathome
Update to 7.6.13
2020-05-09 13:21:29 +00:00
mafft
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mapm3
biology/mapm3: Reformat patches.
2020-09-04 12:24:23 +00:00
migrate
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minimap2
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molden
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mopac
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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
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ncbi-blast+
biology/ncbi-blast+: Upgrade to 2.11.0
2020-11-16 18:25:03 +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
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p5-AcePerl
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p5-Bio-ASN1-EntrezGene
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p5-Bio-Cluster
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p5-Bio-Coordinate
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p5-Bio-Das
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p5-Bio-Das-Lite
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p5-Bio-DB-EMBL
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p5-Bio-DB-NCBIHelper
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p5-Bio-FeatureIO
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p5-Bio-GFF3
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p5-Bio-Glite
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p5-Bio-Graphics
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p5-Bio-MAGETAB
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p5-Bio-NEXUS
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p5-Bio-Phylo
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p5-Bio-SCF
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p5-Bio-Variation
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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
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p5-transdecoder
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p5-TrimGalore
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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
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pear-merger
…
phrap
Sanitize COMMENT per Section 5.6 of the FreeBSD Porter's Handbook (part 1).
2020-05-27 11:59:13 +00:00
phred
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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: Optimise DNA sequencing primer-set combinations
2020-11-15 18:50:17 +00:00
primer3
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prodigal
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prodigy-lig
Unbreak bulk -a
2020-06-13 15:05:44 +00:00
protomol
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psi88
biology/psi88: Unbreak build with GCC 10
2020-07-04 12:15:58 +00:00
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
biology/py-bx-python: Update 0.8.8 -> 0.8.9
2020-06-26 04:17:11 +00:00
py-cutadapt
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py-dnaio
biology/py-dnaio: Upgrade to 0.4.2
2020-05-24 15:23:15 +00:00
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
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py-Genesis-PyAPI
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py-gffutils
Unbreak bulk -a
2020-07-14 07:59:28 +00:00
py-gtfparse
biology/py-gtfparse: Update 1.2.0 -> 1.2.1
2020-08-07 04:13:00 +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
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py-multiqc
Unbreak bulk -a
2020-09-19 14:15:42 +00:00
py-orange3-bioinformatics
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py-orange3-single-cell
Update Sphinx
2020-05-11 23:51:58 +00:00
py-pandas-charm
Clean up some things
2020-05-30 00:57:02 +00:00
py-pyfaidx
biology/py-pyfaidx: Update 0.5.5.2 -> 0.5.9.1
2020-09-13 19:05:30 +00:00
py-pysam
biology/py-pysam: Update 0.16.0 -> 0.16.0.1
2020-11-15 19:26:37 +00:00
py-scikit-bio
biology/py-scikit-bio: Fix build on the i386 architecture
2020-09-24 23:16:26 +00:00
py-xenaPython
biology/py-xenaPython: Update 1.0.10 -> 1.0.14
2020-11-11 05:27:43 +00:00
pyfasta
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python-nexus
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rainbow
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recombine
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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
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seqan1
…
seqan-apps
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seqio
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seqtk
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sim4
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slclust
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smithwaterman
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stacks
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star
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stringtie
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subread
biology/subread: Add -fcommon for clang 11
2020-09-18 00:57:35 +00:00
tabixpp
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
treekin
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treepuzzle
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trimadap
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trimmomatic
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tRNAscan-SE
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ugene
biology/ugene: prepare for Qt5-5.15
2020-05-19 18:00:02 +00:00
vcflib
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
vcftools
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velvet
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viennarna
biology/viennarna: Update 2.4.15 -> 2.4.16
2020-11-11 23:27:38 +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
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Makefile
biology/pooler: Optimise DNA sequencing primer-set combinations
2020-11-15 18:50:17 +00:00