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0a20a7661d
freebsd-ports/biology
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Jason W. Bacon 0a20a7661d biology/kallisto: Upgrade to 0.46.2 
Kallisto no longer builds in hdf5 by default, but it is still required
for some downstream tools like Sleuth.  Forcing it ON for now, but will
disable it in a future upgrade.

Reported by:    portscout
2020-02-15 23:09:19 +00:00
..
abyss biology/abyss: Broken on i386 2020-01-18 19:46:26 +00:00
artemis Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
avida biology/avida: unbreak on powerpc64 2019-10-23 16:25:10 +00:00
babel
bamtools devel/jsoncpp: Update 1.8.1 -> 1.9.2 2020-01-13 21:38:35 +00:00
bcftools math/gsl: update to 2.6 2019-10-25 23:41:34 +00:00
bedtools biology/bedtools: Upgrade to 2.29.2 2019-12-19 01:04:11 +00:00
biococoa
bolt-lmm Fix math/openblas and bump dependent ports 2020-01-30 14:17:44 +00:00
bowtie
bowtie2 Update devel/tbb to 2020.0 and bump dependent ports' revisions [1] 2019-12-26 16:25:22 +00:00
bwa
canu devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
cd-hit
cdbfasta
checkm
clustal-omega
clustalw
consed Mark a few ports BROKEN, unfetchable 2019-11-06 12:48:32 +00:00
cufflinks devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
cytoscape Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
ddocent
diamond biology/diamond: Update to version 0.9.30 2020-02-03 15:55:05 +00:00
dsr-pdb devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
emboss Sprinkle more USES=xorg 2019-11-07 20:19:59 +00:00
exonerate
fasta
fasta3
fastahack biology/fastahack: Upgrade to 1.0.0 2019-10-06 21:34:32 +00:00
fastdnaml
fastool
fastp
fastqc biology/fastqc: Upgrade to 0.11.8 2019-09-21 02:44:54 +00:00
fasttree
fastx-toolkit
figtree
fluctuate
freebayes
garlic Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
gatk biology/gatk: Change from gradle5 to gradle6 2020-02-09 05:57:04 +00:00
gemma Fix math/openblas and bump dependent ports 2020-01-30 14:17:44 +00:00
gff2ps
gmap
gperiodic - Update WWW 2020-01-19 09:30:22 +00:00
graphlan
grappa
groopm
haplohseq devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
hhsuite devel/openmp: update to 9.0.0 2019-09-21 18:59:57 +00:00
hisat2
hmmer biology/hmmer: update to 3.3 2020-01-29 05:55:12 +00:00
htslib
hyphy
igv
infernal biology/infernal: update to 1.1.3 2020-01-27 17:57:14 +00:00
iolib
iqtree biology/iqtree: Update to version 1.6.12 2019-08-27 01:19:11 +00:00
jalview Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
jellyfish Drop C++11 workaround for GCC < 6 after r449590 2019-09-14 22:01:13 +00:00
kallisto biology/kallisto: Upgrade to 0.46.2 2020-02-15 23:09:19 +00:00
lagan
lamarc
libbigwig
libgtextutils
libsbml Clean up Makefile 2020-02-08 19:01:40 +00:00
mafft
mapm3
migrate
minimap2
molden Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
mopac
mothur biology/mothur: Update 1.42.3 -> 1.43.0 2019-10-05 17:04:42 +00:00
mrbayes Mark a few ports BROKEN, unfetchable 2019-11-06 12:48:32 +00:00
mummer
muscle biology/muscle: unbreak in -CURRENT 2020-01-17 16:49:03 +00:00
ncbi-blast+ biology/ncbi-blast+: Upgrade to 2.10.0 2019-12-26 16:21:17 +00:00
ncbi-cxx-toolkit Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
ncbi-toolkit biologi/ncbi-toolkit: Remove dependency on libXp 2019-09-28 10:52:57 +00:00
ngs-sdk biology/ngs-sdk: Update 2.10.1 -> 2.10.2 2020-01-17 07:05:29 +00:00
p5-AcePerl
p5-Bio-ASN1-EntrezGene Update *_DEPENDS 2020-01-08 18:36:30 +00:00
p5-Bio-Cluster Update *_DEPENDS 2019-12-08 16:57:18 +00:00
p5-Bio-Coordinate
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-DB-EMBL Add p5-Bio-DB-EMBL 1.7.4 2019-12-08 16:49:19 +00:00
p5-Bio-DB-NCBIHelper Add p5-Bio-DB-NCBIHelper 1.7.6 2019-12-08 16:49:25 +00:00
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 Update to 1.7.5 2020-01-08 18:36:35 +00:00
p5-BioPerl Update to 1.007007 (1.7.7) 2019-12-08 16:57:23 +00:00
p5-BioPerl-Run Remove outdated CONFLICTS: p5-bioperl-run was renamed to p5-BioPerl-Run over 3 years ago 2020-01-08 18:36:40 +00:00
p5-transdecoder
p5-TrimGalore biology/p5-TrimGalore: Upgrade to 0.6.5 2019-11-26 16:20:12 +00:00
paml biology/paml: Update to version 4.9j 2019-11-22 15:32:40 +00:00
pbbam devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
pbcopper devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
pbseqan biology/unanimity and dependencies: Flag as no longer open source 2019-11-24 15:53:00 +00:00
pear-merger
phrap
phred
phylip Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
phyml biology/phyml: disable -march=native 2019-12-06 13:04:41 +00:00
plinkseq Mark a few ports BROKEN, unfetchable 2019-11-06 12:48:32 +00:00
primer3
prodigal biology/prodigal: Eliminate a very old version from the portscout discovery process 2019-10-12 15:40:21 +00:00
prodigy-lig
protomol Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
psi88
py-biom-format - Limit python version (does not build with 3.7+) 2019-11-08 12:12:42 +00:00
py-biopython
py-bx-python biology/py-bx-python: Update 0.8.6 -> 0.8.8 2020-02-15 20:08:30 +00:00
py-cutadapt biology/py-cutadapt: Upgrade to 2.7 2019-11-23 14:45:53 +00:00
py-dnaio biology/py-dnaio: Upgrade to 0.4.1 2019-11-23 14:40:00 +00:00
py-fastTSNE devel/openmp: update to 9.0.0 2019-09-21 18:59:57 +00:00
py-Genesis-PyAPI
py-gffutils biology/py-gffutils: Update 0.9 -> 0.10 2019-12-31 05:16:09 +00:00
py-gtfparse
py-loompy
py-macs2 biology/py-macs2: Bump revision for previous run dep addition 2020-02-09 14:23:43 +00:00
py-multiqc biology/py-multiqc: Upgrade to 1.8 2019-11-26 16:25:08 +00:00
py-orange3-bioinformatics
py-orange3-single-cell
py-pyfaidx
py-pysam biology/py-pysam: Update 0.15.3 -> 0.15.4 2020-01-23 02:53:09 +00:00
py-xenaPython
pyfasta
python-nexus
rainbow
recombine Fix after gets(3) retirement using gets_s(3). 2019-09-02 05:00:43 +00:00
ruby-bio
rubygem-bio
samtools
seaview biology/seaview: Update version 4.7=>5.0 2020-02-05 18:35:42 +00:00
seqan
seqan1 Fix some misspelled or duplicated LICENSE_* 2019-09-17 19:21:45 +00:00
seqan-apps devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
seqio
seqtk
seqtools Mark a few ports BROKEN, unfetchable 2019-11-06 12:48:32 +00:00
sim4
slclust
smithwaterman
stacks
star biology/star: Upgrade to 2.7.2d 2019-10-06 22:18:31 +00:00
stringtie
t_coffee Mark a few ports BROKEN, unfetchable 2019-11-06 12:48:32 +00:00
tabixpp
tophat devel/boost-*: update to 1.72.0 2019-12-11 17:53:48 +00:00
treekin Fix math/openblas and bump dependent ports 2020-01-30 14:17:44 +00:00
treepuzzle
trimadap
trimmomatic Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
tRNAscan-SE biology/tRNAscan-SE: update to 2.0.5 2020-01-13 17:36:57 +00:00
ugene Mark a few ports BROKEN, unfetchable 2019-11-06 12:48:32 +00:00
vcflib
vcftools
velvet
viennarna biology/viennarna: Update 2.4.13 -> 2.4.14 2020-01-06 04:17:48 +00:00
vsearch
wise a-b: Add missing USES={gnome,php,sdl,xorg} 2019-11-08 09:27:56 +00:00
Makefile Remove expired ports: 2020-01-27 15:34:18 +00:00