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freebsd-ports/biology
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Jason W. Bacon 2730cd269d biology/py-multiqc: Update to 1.9 
Fix runtime error due to incompatibility of 1.8 with latest matplotlib
Drop python2 support
Numerous new features and bug fixes
2021-02-05 01:37:04 +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
For ports on riscv64 that fail the same (or similar ways) to aarch64, mark
2021-01-02 01:46:08 +00:00
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
biology/bedtools: Upgrade to 2.30.0
2021-01-24 18:25:39 +00:00
bioawk
biology/bioawk: BWK awk modified for biological data
2020-06-05 02:45:33 +00:00
biococoa
Return theraven's ports to the pool after safekeeping his commit bit.
2020-03-05 20:49:05 +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
biology/bowtie: Unbreak build with GCC 10
2020-07-04 10:46:08 +00:00
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
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checkm
scipy 1.5.4 is only compatible with python 3.6+
2020-12-24 09:03:39 +00:00
clustal-omega
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clustalw
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cufflinks
- Upgrade math/eigen3 to 3.3.8;
2020-12-12 17:04:37 +00:00
cytoscape
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ddocent
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diamond
biology/diamond: Update to version 2.0.6
2020-12-20 20:21:41 +00:00
dsr-pdb
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edlib
Fix build on GCC-based systems by adding compiler:c++14-lang to USES:
2021-01-20 02:31:33 +00:00
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
biology/fastp: Upgrade to 0.20.1
2020-04-09 16:17:02 +00:00
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
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figtree
Add education virtual category
2020-11-20 07:16:06 +00:00
fluctuate
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freebayes
For ports on riscv64 that fail the same (or similar ways) to aarch64, mark
2021-01-02 01:46:08 +00:00
garlic
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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
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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
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
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 2.5.27
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
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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
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
kallisto
biology/kallisto: Add -lz for pending hdf5 upgrade
2021-01-26 01:34:20 +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
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
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mapm3
biology/mapm3: Reformat patches.
2020-09-04 12:24:23 +00:00
migrate
Mark BROKEN on riscv64 the same as armv*:
2021-01-19 02:26:53 +00:00
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+: 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
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p5-Bio-ASN1-EntrezGene
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p5-Bio-Cluster
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p5-Bio-Coordinate
Cosmetic change
2020-04-02 12:01:30 +00:00
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
Cosmetic change
2020-04-02 12:01:35 +00:00
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
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
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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: Upgrade to 1.76
2021-01-08 22:44:13 +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
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
Drop dependency on devel/openmp
2020-03-08 21:56:36 +00:00
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
Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+
2021-01-30 13:29:58 +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
Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+
2021-01-30 13:29:58 +00:00
py-macs2
biology/py-macs2: Upgrade to 2.2.7.1
2020-04-14 12:13:55 +00:00
py-multiqc
biology/py-multiqc: Update to 1.9
2021-02-05 01:37:04 +00:00
py-orange3-bioinformatics
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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
Update WWW
2020-03-31 23:18:09 +00:00
rampler
Add compiler:c++11-lang to USES to fix build on GCC-based systems:
2021-01-20 02:30:13 +00:00
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
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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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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
biology/stringtie: fix build on GCC architectures
2020-02-23 10:52:44 +00:00
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
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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
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
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velvet
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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
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Makefile
New port: biology/rampler: Standalone module for sampling genomic sequences
2021-01-19 09:49:53 +00:00