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2019Q1
freebsd-ports/biology
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Joseph Mingrone 3b7c3a4880 biology/diamond: Update to version 0.9.24 
Port changes: Tune for package building based on the author's
recommendation.

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.24
2018-12-31 19:00:00 +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 biology/bcftools: update to 1.9 2018-08-02 19:30:57 +00:00
bedtools Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
biococoa Update Objective-C LLVM version to 6.0. 2018-09-26 15:23:37 +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 Multiple ports: 2018-01-31 01:07:07 +00:00
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 Multiple ports: 2018-01-31 01:07:07 +00:00
checkm Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
chemeq
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
clustalx Mark QT4 ports/functionality for removal on 2019-03-15 2018-12-02 15:41:47 +00:00
consed
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 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
emboss
exonerate New port: biology/exonerate: Generic tool for sequence alignment 2018-07-13 07:02:16 +00:00
fasta
fasta3
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
fastqc
fasttree Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
fastx-toolkit biology/fastx-toolkit: Fix build on FreeBSD 12 2018-05-16 15:13:43 +00:00
fluctuate
freebayes Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
garlic Return maho@'s ports to the pool after his commit bit expired. 2018-03-11 11:20:43 +00:00
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 Multiple ports: 2018-01-31 01:07:07 +00:00
gperiodic
grappa
groopm Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
hmmer biology/hmmer: update to 3.2.1 2018-07-11 15:15:03 +00:00
htslib biology/htslib: update to 1.9 2018-08-02 19:27:13 +00:00
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 Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
lagan
lamarc biology/lamarc: Fix build with Clang 6 2018-08-25 03:13:37 +00:00
libgtextutils biology/libgtextutils: Unbreak for FreeBSD 12 2018-03-29 15:41:07 +00:00
libsbml Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +00:00
linux-foldingathome biology/linux-foldingathome: reset maintainer by request 2018-07-27 02:19:43 +00:00
mafft
mapm3
migrate Mark broken on armvX and mips. 2018-03-18 13:48:07 +00:00
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+ Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +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 Fix build failure with base GCC because of double typedefs. 2018-11-05 19:47:42 +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:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-Bio-ASN1-EntrezGene Update to 1.73 2018-10-10 10:23:10 +00:00
p5-Bio-Coordinate Fix every instance of RUN_DEPENDS:=${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 Fix every instance of RUN_DEPENDS:=${BUILD_DEPENDS} in p5 ports, except 2018-10-06 13:06:42 +00:00
p5-BioPerl-Run Fix every instance of RUN_DEPENDS:=${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 biology/paml: Set PORTVERSION directly 2018-04-26 15:36:30 +00:00
pbbam Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
pbcopper Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
pbseqan biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn 2018-04-21 17:21:30 +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 Add DOCS options to ports that should have one. 2018-09-10 13:14:50 +00:00
phylip - Update to 3.697 2018-01-01 08:40:22 +00:00
phyml Change 4 ports from net/mpich2 to net/mpich 2018-09-22 18:00:24 +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
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 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 Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
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 Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +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 Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
py-orange3-single-cell Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +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 0.15.0 -> 0.15.1 2018-09-17 17:40:28 +00:00
pycogent Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +00:00
pyfasta Bump PORTREVISION for ports depending on the canonical version of GCC 2018-12-12 01:35:33 +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 biology/samtools: update to 1.9 2018-08-02 19:28:36 +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 Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +00:00
seqio
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 2018-12-12 01:35:33 +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 2018-12-12 01:35:33 +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 2018-12-12 01:35:33 +00:00
tabixpp biology/tabixpp: C++ wrapper to tabix indexer 2018-04-14 23:52:16 +00:00
treepuzzle
trimadap Mark as broken on aarch64, and, where appropriate, armvX. 2018-06-21 23:52:37 +00:00
trimmomatic Multiple ports: 2018-01-31 01:07:07 +00:00
tRNAscan-SE - Unbreak by adding missing pkg-plist 2018-09-28 00:12:48 +00:00
ugene Update Qt5 to 5.12.0 2018-12-16 14:49:16 +00:00
unanimity Change cmake default behaviour to outsource. 2018-12-25 20:25:39 +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
wise
Makefile Remove expired ports: 2018-12-21 13:19:02 +00:00