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cab08e0d6d
freebsd-ports/biology
History
Jason W. Bacon c4b007e3b2 biology/unanimity: Remove erroneous BROKEN 
Unsure why this was marked unfetchable.  Fetch works fine and the port is
still useful, though it cannot be upgraded to newer releases, which are
closed-source.
2019-11-28 05:46:04 +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 2.29.0 2019-09-13 13:21:59 +00:00
biococoa
bolt-lmm devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
bowtie Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
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 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
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 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
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 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
fastqc biology/fastqc: Upgrade to 0.11.8 2019-09-21 02:44:54 +00:00
fasttree Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
fastx-toolkit
figtree
fluctuate
freebayes Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
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 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
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 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
igv biology/igv: Update 2.5.2 -> 2.5.3 2019-06-01 20:49:20 +00:00
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 New port: biology/libbigwig: C library for handling bigWig files (containing genomic data) 2019-07-11 17:05:22 +00:00
libgtextutils
libsbml Use USES=pathfix 2019-06-22 21:48:14 +00:00
mafft
mapm3
migrate
minimap2 biology/minimap2: Upgrade to 2.17 2019-05-05 14:56:07 +00:00
molden Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
mopac Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
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 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
muscle
ncbi-blast+ Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +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 2.9.6 -> 2.10.0 2019-08-31 15:09:47 +00:00
p5-AcePerl
p5-Bio-ASN1-EntrezGene
p5-Bio-Cluster
p5-Bio-Coordinate
p5-Bio-Das
p5-Bio-Das-Lite
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-BioPerl Update to 1.007006 (1.7.6) 2019-09-07 22:44:02 +00:00
p5-BioPerl-Run
p5-transdecoder Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
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: update to 3.3.20190909 2019-09-10 21:04:16 +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 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
protomol Add USES=xorg USES=gl, ports categories b 2019-11-04 21:08:20 +00:00
psi88 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
py-biom-format - Limit python version (does not build with 3.7+) 2019-11-08 12:12:42 +00:00
py-biopython Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
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 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
py-loompy Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
py-macs2 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
py-multiqc biology/py-multiqc: Upgrade to 1.8 2019-11-26 16:25:08 +00:00
py-orange3-bioinformatics Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
py-orange3-single-cell Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
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 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
pyfasta Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
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 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
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 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
treepuzzle
trimadap biology/trimadap: Mark only for amd64 and i386 2019-05-11 00:18:24 +00:00
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 2.0.3 2019-06-08 01:31:18 +00:00
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 biology/vsearch: Update to 2.13.4 2019-05-11 13:42:33 +00:00
wise a-b: Add missing USES={gnome,php,sdl,xorg} 2019-11-08 09:27:56 +00:00
Makefile Remove expired ports: 2019-10-16 15:29:32 +00:00