mirror/freebsd-ports
1
0
Fork 0
mirror of https://git.FreeBSD.org/ports.git synced 2024-12-23 04:23:08 +00:00
Code Issues Releases Activity
695a189942
freebsd-ports/biology
History
Sunpoet Po-Chuan Hsieh 20b6ec5afb Update to 1.007006 (1.7.6) 
- Remove PGTEST and SQLITETEST options: DBD::Pg and DBD::SQLite have been removed from BioPerl by upstream for the move of modules and programs into separate distributions

Changes:	https://metacpan.org/changes/distribution/BioPerl
2019-09-07 22:44:02 +00:00
..
abyss devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
artemis
avida
babel
bamtools
bcftools Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
bedtools Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +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 biology/bowtie2: Clarify CPU-specificity 2019-04-24 17:41:27 +00:00
bwa
canu devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +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
chemeq Mark BROKEN: unfetchable 2019-08-04 08:31:22 +00:00
clustal-omega
clustalw
consed Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
cufflinks devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
cytoscape
ddocent Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
diamond Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
dsr-pdb devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
emboss Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +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
fastdnaml
fastool
fastp Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
fastqc
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
gatk biology/gatk: Update 4.0.11.0 -> 4.1.2.0-43 2019-07-26 18:03:08 +00:00
gemma Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
gff2ps
gmap Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
gperiodic biology/gperiodic: fix NLS and other rough edges 2019-08-23 15:26:55 +00:00
graphlan
grappa
groopm Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
hhsuite biology/hhsuite: fix build on powerpc64 2019-08-05 14:23:23 +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 - Fix build in head i386 2019-04-01 19:33:15 +00:00
iqtree biology/iqtree: Update to version 1.6.12 2019-08-27 01:19:11 +00:00
jalview
jellyfish Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
kallisto Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +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
linux-foldingathome Mark BROKEN: unfetchable 2019-08-04 08:31:22 +00:00
mafft
mapm3
migrate
minimap2 biology/minimap2: Upgrade to 2.17 2019-05-05 14:56:07 +00:00
molden Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
mopac Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
mothur Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
mrbayes Update devel/readline to 8.0 2019-04-09 14:04:49 +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 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
ncbi-toolkit Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +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 Fix typo 2019-04-23 14:11:50 +00:00
p5-Bio-NEXUS
p5-Bio-Phylo
p5-Bio-SCF - Add LICENSE 2019-03-30 09:01:08 +00:00
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 0.6.1 2019-03-24 21:44:17 +00:00
paml
pbbam devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
pbcopper devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
pbseqan
pear-merger
phrap
phred Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
phylip
phyml - Update to 3.3.20190321 2019-05-20 09:17:29 +00:00
plinkseq
primer3
prodigal
prodigy-lig Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
protomol
psi88 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
py-biom-format Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +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 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
py-cutadapt biology/py-cutadapt: Upgrade to 2.3 2019-04-27 01:26:17 +00:00
py-dnaio
py-fastTSNE Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
py-Genesis-PyAPI
py-gffutils Bump a few PORTREVISIONs after r498529 2019-04-10 06:18:31 +00:00
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-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 Bump a few PORTREVISIONs after r498529 2019-04-10 06:18:31 +00:00
py-pysam biology/py-pysam: Update 0.15.2 -> 0.15.3 2019-08-31 15:49:18 +00:00
py-xenaPython New port: biology/py-xenaPython: API for Xena Hub to access genetic information shared through the hub 2019-04-12 17:01:10 +00:00
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
seqan
seqan1
seqan-apps devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
seqio
seqtk
seqtools Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +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 Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
stringtie
t_coffee Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
tabixpp
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
tRNAscan-SE biology/tRNAscan-SE: Update to 2.0.3 2019-06-08 01:31:18 +00:00
ugene
unanimity devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
vcflib
vcftools
velvet
viennarna Bump PORTREVISION for ports depending on the canonical version of GCC 2019-07-26 20:46:53 +00:00
vsearch biology/vsearch: Update to 2.13.4 2019-05-11 13:42:33 +00:00
wise Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
Makefile New port: biology/libbigwig: C library for handling bigWig files (containing genomic data) 2019-07-11 17:05:22 +00:00