1
0
mirror of https://git.FreeBSD.org/ports.git synced 2024-12-23 04:23:08 +00:00
freebsd-ports/biology
Jason W. Bacon d34aa59b6f biology/bedtools: Upgrade to 2.29.1
Several important bug fixes.

Reported by:    portscout
2019-12-11 15:13:20 +00:00
..
abyss devel/openmp: update to 9.0.0 2019-09-21 18:59:57 +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
bcftools math/gsl: update to 2.6 2019-10-25 23:41:34 +00:00
bedtools biology/bedtools: Upgrade to 2.29.1 2019-12-11 15:13:20 +00:00
biococoa
bolt-lmm devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
bowtie
bowtie2 Update devel/tbb to 2019.8 and bump dependent ports' revisions 2019-09-25 10:03:49 +00:00
bwa
canu biology/canu: Upgrade to 1.9 2019-11-08 14:03:15 +00:00
cd-hit
cdbfasta
checkm biology/checkm: Update 1.0.17 -> 1.0.18 2019-08-19 08:25:29 +00:00
clustal-omega
clustalw
consed Mark a few ports BROKEN, unfetchable 2019-11-06 12:48:32 +00:00
cufflinks devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +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 v0.9.29 2019-11-20 17:14:29 +00:00
dsr-pdb devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
emboss Sprinkle more USES=xorg 2019-11-07 20:19:59 +00:00
exonerate
fasta Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
fasta3 Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
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 Create devel/gradle5 in preparation of devel/gradle update 2019-11-20 09:51:43 +00:00
gemma math/gsl: update to 2.6 2019-10-25 23:41:34 +00:00
gff2ps
gmap Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
gperiodic a-b: Add missing USES={gnome,php,sdl,xorg} 2019-11-08 09:27:56 +00:00
graphlan
grappa
groopm
haplohseq biology/haplohseq: Switch to distfile with example data 2019-11-17 15:00:13 +00:00
hhsuite devel/openmp: update to 9.0.0 2019-09-21 18:59:57 +00:00
hisat2
hmmer Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
htslib
hyphy
igv
infernal
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 0.46.1 2019-11-06 00:18:14 +00:00
lagan Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
lamarc
libbigwig
libgtextutils
libsbml
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
ncbi-blast+
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 2.9.6 -> 2.10.0 2019-08-31 15:09:47 +00:00
p5-AcePerl
p5-Bio-ASN1-EntrezGene Install Bio::SeqIO::entrezgene 2019-12-08 16:57:13 +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 Add p5-Bio-Variation 1.7.4 2019-12-08 16:49:31 +00:00
p5-BioPerl Update to 1.007007 (1.7.7) 2019-12-08 16:57:23 +00:00
p5-BioPerl-Run
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 biology/unanimity and dependencies: Flag as no longer open source 2019-11-24 15:53:00 +00:00
pbcopper biology/unanimity and dependencies: Flag as no longer open source 2019-11-24 15:53:00 +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 Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
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 0.8.4 -> 0.8.6 2019-11-23 05:53:50 +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
py-gtfparse
py-loompy
py-macs2
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 0.15.2 -> 0.15.3 2019-08-31 15:49:18 +00:00
py-xenaPython
pycogent
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 Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
seaview Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
seqan
seqan1 Fix some misspelled or duplicated LICENSE_* 2019-09-17 19:21:45 +00:00
seqan-apps devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +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 biology/tophat: Fast splice junction mapper for RNA-Seq reads 2019-09-27 00:49:48 +00:00
treekin
treepuzzle
trimadap
trimmomatic Clean up after java/openjdk6 and java/openjdk6-jre removal 2019-11-26 21:46:12 +00:00
tRNAscan-SE
ugene Mark a few ports BROKEN, unfetchable 2019-11-06 12:48:32 +00:00
unanimity biology/unanimity: Remove erroneous BROKEN 2019-11-28 05:46:04 +00:00
vcflib
vcftools
velvet
viennarna Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
vsearch
wise a-b: Add missing USES={gnome,php,sdl,xorg} 2019-11-08 09:27:56 +00:00
Makefile Add p5-Bio-Variation 1.7.4 2019-12-08 16:49:31 +00:00