Kurt Jaeger bc7e4c2f4a biology/gperiodic: fix NLS and other rough edges ... PR: 239642 Submitted by: Walter Schwarzenfeld <w.schwarzenfeld@utanet.at> Reported by: bapt		2019-08-23 15:26:55 +00:00
..
abyss	devel/boost-*: update to 1.71.0	2019-08-19 15:35:27 +00:00
artemis	biology/artemis: Update 9 -> 17.0.1-11	2018-06-11 17:45:56 +00:00
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	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	Move Objective-C ports to the v2 GNUstep ABI.	2019-02-03 15:37:58 +00:00
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	Multiple ports:	2018-01-31 01:07:07 +00:00
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	Multiple ports:	2018-01-31 01:07:07 +00:00
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	biology/clustal-omega: Multiple alignment of nucleic acid and protein, replaces clustalw	2018-05-21 22:15:26 +00:00
clustalw	biology/clustalw: Fix license, take maintainership	2018-05-21 01:13:40 +00:00
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	biology/cytoscape: Fix license	2018-08-12 06:29:51 +00:00
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	New port: biology/exonerate: Generic tool for sequence alignment	2018-07-13 07:02:16 +00:00
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: Utility for indexing and sequence extraction from FASTA files	2018-04-16 14:50:46 +00:00
fastdnaml
fastool	Multiple ports:	2018-01-31 01:07:07 +00:00
fastp	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
fastqc	[new port] biology/fastqc: Quality control tool for high throughput sequence data	2017-11-30 22:54:29 +00:00
fasttree	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
fastx-toolkit	biology/fastx-toolkit: Fix build on FreeBSD 12	2018-05-16 15:13:43 +00:00
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	2019-07-26 20:46:53 +00:00
garlic	Return maho@'s ports to the pool after his commit bit expired.	2018-03-11 11:20:43 +00:00
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	biology/gff2ps: update 0.98d to 0.98l	2018-12-19 17:34:29 +00:00
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	New port: biology/graphlan: High-quality circular representations of taxonomic, phylogenetic trees	2019-02-03 20:13:26 +00:00
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	New port: biology/hisat2: Program for mapping next-generation sequencing reads	2019-01-11 16:02:05 +00:00
hmmer	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
htslib	biology/htslib: update to 1.9	2018-08-02 19:27:13 +00:00
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	Allow building on powerpc64.	2018-09-27 23:02:56 +00:00
iolib	- Fix build in head i386	2019-04-01 19:33:15 +00:00
iqtree	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +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	biology/lamarc: Fix build with Clang 6	2018-08-25 03:13:37 +00:00
libbigwig	New port: biology/libbigwig: C library for handling bigWig files (containing genomic data)	2019-07-11 17:05:22 +00:00
libgtextutils	biology/libgtextutils: Unbreak for FreeBSD 12	2018-03-29 15:41:07 +00:00
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	Mark broken on armvX and mips.	2018-03-18 13:48:07 +00:00
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	Mark this port as not buildable on powerpc64:	2019-06-25 12:17:04 +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 typo	2019-04-23 14:11:50 +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	- Add LICENSE	2019-03-30 09:01:08 +00:00
p5-BioPerl	Update to 1.007005 (1.7.5)	2019-08-11 16:49:24 +00:00
p5-BioPerl-Run	Update to 1.007003	2019-02-20 20:46:58 +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 0.6.1	2019-03-24 21:44:17 +00:00
paml	biology/paml: Update to version 4.9i	2019-02-26 15:12:42 +00:00
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	biology/pbseqan: Mark deprecated	2019-02-20 01:53:35 +00:00
pear-merger	Mark as broken on aarch64, and, where appropriate, armvX.	2018-06-21 23:52:37 +00:00
phrap	Add DOCS options to ports that should have one.	2018-09-10 13:14:50 +00:00
phred	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
phylip	- Update to 3.697	2018-01-01 08:40:22 +00:00
phyml	- Update to 3.3.20190321	2019-05-20 09:17:29 +00:00
plinkseq	Multiple ports:	2018-01-31 01:07:07 +00:00
primer3	biology/primer3: Fix build with Clang 6	2018-08-25 03:35:46 +00:00
prodigal	New port: biology/prodigal: Protein-coding gene prediction for prokaryotic genomes	2019-02-03 18:08:14 +00:00
prodigy-lig	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
protomol	biology/protomol: Fix doubled USES overwriting the old value	2018-08-25 03:47:25 +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	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	biology/py-dnaio: Read and write FASTQ and FASTA	2019-03-24 19:40:26 +00:00
py-fastTSNE	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
py-Genesis-PyAPI	Use PY_FLAVOR for dependencies.	2018-06-20 17:05:41 +00:00
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 0.15.1 -> 0.15.2	2019-01-26 04:15:54 +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	- Update to 1.63	2018-09-22 08:54:58 +00:00
rainbow	biology/rainbow: Efficient clustering and assembling of short reads	2018-04-02 16:50:46 +00:00
recombine
ruby-bio
rubygem-bio	Update to 1.5.2	2018-09-21 18:08:24 +00:00
samtools	Convert to UCL & cleanup pkg-message (categories a-c)	2019-08-13 16:00:39 +00:00
seaview	biology/seaview: Fix build with Clang 6	2018-09-08 09:01:35 +00:00
seqan	biology/seqan-apps, biology/seqan: Update to 2.4.0	2018-03-10 06:21:37 +00:00
seqan1
seqan-apps	devel/boost-*: update to 1.71.0	2019-08-19 15:35:27 +00:00
seqio	- Switch to options helpers	2017-11-26 09:00:21 +00:00
seqtk	biology/seqtk: Tool for processing sequences in FASTA/FASTQ format	2018-04-03 20:57:05 +00:00
seqtools	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
sim4
slclust	Multiple ports:	2018-01-31 01:07:07 +00:00
smithwaterman	biology/smithwaterman: Smith-waterman-gotoh alignment algorithm	2018-04-15 17:45:52 +00:00
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	New port: biology/stringtie: Transcript assembly and quantification for RNA-seq	2018-07-11 21:32:39 +00:00
t_coffee	Bump PORTREVISION for ports depending on the canonical version of GCC	2019-07-26 20:46:53 +00:00
tabixpp	biology/tabixpp: C++ wrapper to tabix indexer	2018-04-14 23:52:16 +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	Multiple ports:	2018-01-31 01:07:07 +00:00
tRNAscan-SE	biology/tRNAscan-SE: Update to 2.0.3	2019-06-08 01:31:18 +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	devel/boost-*: update to 1.71.0	2019-08-19 15:35:27 +00:00
vcflib	Mark these ports as broken on aarch64.	2018-06-22 00:03:08 +00:00
vcftools	biology/vcftools: Update to 0.1.16, a security release	2018-08-04 01:29:29 +00:00
velvet	- Convert to option helper install target (add OPTIONS_DEFINE=DOCS	2018-01-11 18:09:00 +00:00
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