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0181afcee3
freebsd-ports/biology
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Sunpoet Po-Chuan Hsieh 0181afcee3 Update to 1.007004 (1.7.4) 
- Add LICENSE_FILE
- Use USES=shebangfix
- Use COPYTREE_SHARE instead of CP -R
- Take maintainership

Changes:	https://metacpan.org/changes/distribution/BioPerl
2019-02-20 20:46:53 +00:00
..
artemis
avida Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +00:00
babel
bamtools Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +00:00
bcftools
bedtools Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
biococoa Move Objective-C ports to the v2 GNUstep ABI. 2019-02-03 15:37:58 +00:00
bowtie Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
bowtie2 Update devel/tbb to version 2019.1 and bump dependent ports' revisions 2018-10-11 14:47:13 +00:00
bwa
canu Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
cd-hit Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
cdbfasta
checkm biology/checkm: Update 1.0.12 -> 1.0.13 2019-02-09 22:58:09 +00:00
chemeq
clustal-omega
clustalw
clustalx Mark QT4 ports/functionality for removal on 2019-03-15 2018-12-02 15:41:47 +00:00
consed
cytoscape
ddocent Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
diamond biology/diamond: Update to version 0.9.24 2018-12-31 19:00:00 +00:00
dsr-pdb biology/dsr-pdb: Correct typo 2019-02-05 19:01:59 +00:00
emboss
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastqc
fasttree Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
fastx-toolkit
figtree New port: biology/figtree: Graphical viewer of phylogenetic trees 2019-02-03 21:14:38 +00:00
fluctuate
freebayes Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
garlic
gatk devel/gradle: Update to 5.0 2018-12-04 17:53:46 +00:00
gff2ps biology/gff2ps: update 0.98d to 0.98l 2018-12-19 17:34:29 +00:00
gmap
gperiodic
graphlan New port: biology/graphlan: High-quality circular representations of taxonomic, phylogenetic trees 2019-02-03 20:13:26 +00:00
grappa
groopm biology/groopm fails to build with python3 2019-01-07 09:44:42 +00:00
hisat2 New port: biology/hisat2: Program for mapping next-generation sequencing reads 2019-01-11 16:02:05 +00:00
hmmer vec_splats function is not supported by base GCC. Add USES=compiler:c11 2019-02-18 01:30:24 +00:00
htslib
hyphy Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +00:00
igv devel/gradle: Update to 5.0 2018-12-04 17:53:46 +00:00
infernal Allow building on powerpc64. 2018-09-27 23:02:56 +00:00
iolib Remove the incorrect typedefs to fix build on tier-2. 2018-11-05 19:45:23 +00:00
iqtree biology/iqtree: switch to outsource cmake build 2018-12-27 18:34:44 +00:00
jalview
jellyfish Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
kallisto Update science/hdf5 to 1.10.4 2019-01-05 22:46:53 +00:00
lagan
lamarc
libgtextutils
libsbml Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +00:00
linux-foldingathome
mafft
mapm3
migrate
molden Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
mopac Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
mrbayes
mummer Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
muscle
ncbi-blast+ Update dns/libidn2 to 2.1.1 2019-02-09 23:25:36 +00:00
ncbi-cxx-toolkit Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
ncbi-toolkit Update dns/libidn2 to 2.1.1 2019-02-09 23:25:36 +00:00
ngs-sdk biology/ngs-sdk: Update 2.9.2 -> 2.9.3 2018-10-18 21:38:21 +00:00
p5-AcePerl Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-ASN1-EntrezGene Update to 1.73 2018-10-10 10:23:10 +00:00
p5-Bio-Cluster Add p5-Bio-Cluster 1.7.3 2019-02-20 20:46:37 +00:00
p5-Bio-Coordinate Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Das Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Das-Lite Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-FeatureIO Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-GFF3 Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Glite Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Graphics Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-MAGETAB Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-NEXUS Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-Phylo Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-SCF Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-BioPerl Update to 1.007004 (1.7.4) 2019-02-20 20:46:53 +00:00
p5-BioPerl-Run Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-transdecoder Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
p5-TrimGalore
paml
pbbam biology/pbbam: Upgrade to 0.18.0 release 2019-02-19 23:03:41 +00:00
pbcopper biology/pbcopper: Upgrade to 0.4.1 release 2019-02-19 22:20:11 +00:00
pbseqan biology/pbseqan: Mark deprecated 2019-02-20 01:53:35 +00:00
pear-merger
phrap
phred
phylip
phyml Change 4 ports from net/mpich2 to net/mpich 2018-09-22 18:00:24 +00:00
plinkseq
primer3
prodigal New port: biology/prodigal: Protein-coding gene prediction for prokaryotic genomes 2019-02-03 18:08:14 +00:00
prodigy-lig New port: biology/prodigy-lig: Prediction of protein-small molecule binding affinities 2019-02-03 18:49:23 +00:00
protomol
psi88 Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
py-biom-format Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
py-biopython - Update to 1.73 2018-12-22 04:54:51 +00:00
py-bx-python Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
py-cutadapt biology/py-cutadapt: Upgrade to 1.18 2018-09-20 14:10:52 +00:00
py-fastTSNE New port: biology/py-fastTSNE: Fast, parallel implementations of t-SNE 2018-12-15 08:58:05 +00:00
py-Genesis-PyAPI
py-gffutils New port: biology/py-gffutils: Work with GFF and GTF files in a flexible database framework 2018-10-19 02:06:53 +00:00
py-gtfparse Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
py-loompy biology/py-loompy: Update 2.0.16 -> 2.0.17 2019-02-02 21:38:48 +00:00
py-macs2 Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
py-orange3-bioinformatics Fix Qt5 symbol version scripts to put the catch-all clause first. When 2019-01-16 11:13:44 +00:00
py-orange3-single-cell Fix Qt5 symbol version scripts to put the catch-all clause first. When 2019-01-16 11:13:44 +00:00
py-pyfaidx biology/py-pyfaidx: Update 0.5.5.1 -> 0.5.5.2 2018-10-28 04:34:14 +00:00
py-pysam biology/py-pysam: Update 0.15.1 -> 0.15.2 2019-01-26 04:15:54 +00:00
pycogent Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
pyfasta - Update WWW 2019-02-07 09:30:40 +00:00
python-nexus - Update to 1.63 2018-09-22 08:54:58 +00:00
rainbow
recombine
ruby-bio
rubygem-bio Update to 1.5.2 2018-09-21 18:08:24 +00:00
samtools
seaview
seqan
seqan1
seqan-apps Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +00:00
seqio
seqtk
seqtools biology/seqtools: fix build on current, if lld is lld7 2019-01-07 19:54:40 +00:00
sim4
slclust
smithwaterman
stacks biology/stacks: Upgrade to 2.3 2019-01-12 15:53:00 +00:00
stringtie
t_coffee Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
tabixpp
treepuzzle
trimadap
trimmomatic
tRNAscan-SE - Unbreak by adding missing pkg-plist 2018-09-28 00:12:48 +00:00
ugene Fix Qt5 symbol version scripts to put the catch-all clause first. When 2019-01-16 11:13:44 +00:00
unanimity biology/unanimity: Upgrade to 3.4.0 2019-02-20 01:36:51 +00:00
vcflib
vcftools
velvet
wise
Makefile Add p5-Bio-Cluster 1.7.3 2019-02-20 20:46:37 +00:00