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Code Issues Releases Activity
freebsd-ports/biology
History
Yuri Victorovich 797bbee24e biology/py-pysam: Update 0.15.3 -> 0.15.4 
Reported by:	portscout
2020-01-23 02:53:09 +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
devel/boost-*: update to 1.72.0
2019-12-11 17:53:48 +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 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
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 1.72.0
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
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 1.72.0
2019-12-11 17:53:48 +00:00
emboss
Sprinkle more USES=xorg
2019-11-07 20:19:59 +00:00
exonerate
…
fasta
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
biology/gatk: Update 4.1.3.0 -> 4.1.4.1
2020-01-20 02:12:37 +00:00
gemma
math/openblas: Update to 0.3.7
2020-01-21 22:03:19 +00:00
gff2ps
…
gmap
Convert to UCL & cleanup pkg-message (categories a-c)
2019-08-13 16:00:39 +00:00
gperiodic
- Update WWW
2020-01-19 09:30:22 +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
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
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
…
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
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
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
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
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
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
biology/py-gffutils: Update 0.9 -> 0.10
2019-12-31 05:16:09 +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
biology/py-macs2: Upgrade to 2.2.6
2020-01-11 14:20:00 +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 0.15.3 -> 0.15.4
2020-01-23 02:53:09 +00:00
py-xenaPython
…
pycogent
Deprecate a few ports
2019-12-26 07:54:28 +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 1.72.0
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
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
devel/boost-*: update to 1.72.0
2019-12-11 17:53:48 +00:00
treekin
Bump PORTREVISION for ports depending on the canonical version of GCC
2019-07-26 20:46:53 +00:00
treepuzzle
…
trimadap
…
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
unanimity
Mark a few ports broken (unfetchable)
2020-01-05 10:26:04 +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
Add p5-Bio-Variation 1.7.4
2019-12-08 16:49:31 +00:00