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freebsd-ports/biology
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Tobias C. Berner 4e896a50f8 math/gsl: update to 2.6 
- math/p5-Math-GSL does not seem to have any upstream activity to make it work with this version -> mark it broken
  - this also breaks the two consumers of this port

- biology/gemma: has a conflict with cblas, and is makred broken.

PR:		241363
Exp-run by:	antoine
2019-10-25 23:41:34 +00:00
..
abyss devel/openmp: update to 9.0.0 2019-09-21 18:59:57 +00:00
artemis
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 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
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 biology/diamond: Update to version 0.9.26 2019-09-18 18:45:09 +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 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
gatk biology/gatk: Update 4.0.11.0 -> 4.1.2.0-43 2019-07-26 18:03:08 +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 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
haplohseq biology/haplohseq: Identify regions of allelic imbalance 2019-09-16 01:07:31 +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
infernal
iolib
iqtree biology/iqtree: Update to version 1.6.12 2019-08-27 01:19:11 +00:00
jalview
jellyfish Drop C++11 workaround for GCC < 6 after r449590 2019-09-14 22:01:13 +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
libgtextutils
libsbml
mafft
mapm3
migrate
minimap2
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 biology/mothur: Update 1.42.3 -> 1.43.0 2019-10-05 17:04:42 +00:00
mrbayes
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 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 0.6.4 2019-09-21 02:51:26 +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 biology/phyml: update to 3.3.20190909 2019-09-10 21:04:16 +00:00
plinkseq
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
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 2.5 2019-09-13 13:17:26 +00:00
py-dnaio
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: Aggregate bioinformatics analysis reports 2019-09-23 16:09:30 +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
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 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 biology/star: Upgrade to 2.7.2d 2019-10-06 22:18:31 +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
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
trimmomatic biology/trimmomatic: Upgrade to 0.39 2019-09-14 14:45:49 +00:00
tRNAscan-SE
ugene
unanimity devel/boost-*: update to 1.71.0 2019-08-19 15:35:27 +00:00
vcflib
vcftools
velvet
viennarna math/gsl: update to 2.6 2019-10-25 23:41:34 +00:00
vsearch
wise Convert to UCL & cleanup pkg-message (categories a-c) 2019-08-13 16:00:39 +00:00
Makefile Remove expired ports: 2019-10-16 15:29:32 +00:00