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freebsd-ports/biology
History
Rene Ladan 048dda0400 Remove expired ports: 
2018-08-16 net/traceroute: Upstream gone
2018-08-15 net/e169-stats: unknown license
2018-08-15 net/l4ip: unknown license
2018-08-15 net/dhcprelay: unknown license
2018-08-15 emulators/m2000: unknown license
2018-08-15 textproc/ant-xinclude-task: unknown license
2018-08-15 textproc/bomstrip: unknown license
2018-08-15 x11-fonts/ecofont: unknown license
2018-08-15 mail/roundcube-groupvice: unknown license
2018-08-15 security/pft: unknown license
2018-08-15 devel/kickassembler: unknown license
2018-08-15 devel/gdbmods: unknown license
2018-08-15 devel/as31: unknown license
2018-08-15 databases/dbf2mysql: unknown license
2018-08-15 misc/xpns: unknown license
2018-08-15 misc/amfm: unknown license
2018-08-15 games/smashbattle: unknown license
2018-08-15 games/syobon: unknown license
2018-08-15 games/optimax: unknown license
2018-08-15 games/xgospel: unknown license
2018-08-15 biology/blat: unknown license
2018-08-15 x11-clocks/swisswatch: unknown license
2018-08-15 palm/ppmtoTbmp: unknown license
2018-08-15 dns/ghtool: unknown license
2018-08-15 x11-themes/beastie: unknown license
2018-08-15 converters/uudx: unknown license
2018-08-15 sysutils/areca-cli: unknown license
2018-08-16 20:28:32 +00:00
..
artemis biology/artemis: Update 9 -> 17.0.1-11 2018-06-11 17:45:56 +00:00
avida Try to bring some consistency to ports that have x86-specific pieces. 2017-12-21 10:23:19 +00:00
babel
bamtools biology/bamtools: API and toolkit for handling BAM files 2018-03-28 13:26:31 +00:00
bcftools biology/bcftools: update to 1.9 2018-08-02 19:30:57 +00:00
bedtools biology/bedtools: Fix Makefile to respect PREFIX 2018-06-16 17:55:01 +00:00
biococoa Fix configure options for gnustep-make 2017-12-03 12:23:53 +00:00
bowtie Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
bowtie2 biology/bowtie2: Upgrade to 2.3.3.1 2017-11-30 02:59:16 +00:00
bwa Multiple ports: 2018-01-31 01:07:07 +00:00
canu devel/boost-*: update to 1.68.0 2018-08-09 06:58:30 +00:00
cd-hit Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
cdbfasta Multiple ports: 2018-01-31 01:07:07 +00:00
chemeq biology/chemeq: fix build on GCC (taken from dports) 2016-12-18 04:22:26 +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
clustalx Replace bsd.qt.mk by Uses/qt.mk and Uses/qt-dist.mk 2018-06-28 17:39:53 +00:00
consed
cytoscape biology/cytoscape: Fix license 2018-08-12 06:29:51 +00:00
ddocent biology/ddocent: Bash pipeline for RAD sequencing 2018-04-20 01:34:05 +00:00
diamond biology/diamond: Update to version 0.9.22 2018-05-14 17:17:11 +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 [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 2018-07-29 22:18:44 +00:00
fastx-toolkit biology/fastx-toolkit: Fix build on FreeBSD 12 2018-05-16 15:13:43 +00:00
fluctuate
freebayes Mark as broken on aarch64, and, where appropriate, armvX. 2018-06-21 23:52:37 +00:00
garlic Return maho@'s ports to the pool after his commit bit expired. 2018-03-11 11:20:43 +00:00
gff2ps
gmap Multiple ports: 2018-01-31 01:07:07 +00:00
gperiodic Remove libintl.so.9 compatibility link that was added in r374303 to 2016-12-08 19:52:19 +00:00
grappa
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 biology/hyphy: Update to version 2.3.13 2018-05-22 22:55:18 +00:00
igv New port: biology/igv: Visualization tool for genomic datasets 2018-06-25 23:56:00 +00:00
infernal Add new port: biology/infernal 2018-06-06 15:15:18 +00:00
iolib Mark various ports broken on mips64 and, where appropriate, mips. 2018-07-02 00:47:14 +00:00
iqtree Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
jalview
jellyfish Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
kallisto Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
lagan
lamarc biology/lamarc: Fix build on DF (taken from dports) 2016-12-18 04:34:33 +00:00
libgtextutils biology/libgtextutils: Unbreak for FreeBSD 12 2018-03-29 15:41:07 +00:00
libsbml - Update to 5.17.0 2018-06-25 01:37:52 +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 2018-07-29 22:18:44 +00:00
mopac Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
mrbayes Update devel/readline to 7.0 patch 3 2017-06-27 13:46:53 +00:00
mummer - Fix installing scripts and support binaries 2017-10-30 02:27:23 +00:00
muscle
ncbi-blast+ Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
ncbi-toolkit Remove libjpeg.so.11 compatibility link that was added in r374303 to 2016-12-08 16:39:11 +00:00
ngs-sdk Mark as broken on aarch64. 2018-06-25 05:04:46 +00:00
njplot biology/njplot: Add site in MASTER_SITES because package builders are 2016-11-28 15:19:42 +00:00
p5-AcePerl Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-ASN1-EntrezGene Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-Coordinate Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-Das Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-Das-Lite Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-FeatureIO Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-GFF3 Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-Glite Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-Graphics Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-MAGETAB Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-NEXUS Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-Phylo Update WWW 2018-05-27 20:15:16 +00:00
p5-Bio-SCF Update WWW 2018-05-27 20:15:16 +00:00
p5-BioPerl Fix license information for portgs that use "the same license as Perl". 2017-09-15 08:58:46 +00:00
p5-BioPerl-Run Update to 1.007002 2017-09-15 19:17:44 +00:00
p5-transdecoder Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
p5-TrimGalore [new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming 2017-12-09 13:23:32 +00:00
paml biology/paml: Set PORTVERSION directly 2018-04-26 15:36:30 +00:00
pbbam devel/boost-*: update to 1.68.0 2018-08-09 06:58:30 +00:00
pbcopper devel/boost-*: update to 1.68.0 2018-08-09 06:58:30 +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
phred
phylip - Update to 3.697 2018-01-01 08:40:22 +00:00
phyml biology/phyml: update to v3.3.20180621 2018-06-23 15:53:54 +00:00
plinkseq Multiple ports: 2018-01-31 01:07:07 +00:00
primer3
protomol Revision bump of all ports with USE_GL after consolidation of mesa-libs 2017-05-23 05:03:14 +00:00
psi88 Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +00:00
py-biom-format Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
py-biopython Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
py-bx-python Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
py-cutadapt Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
py-Genesis-PyAPI Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
py-macs2 Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-orange3-bioinformatics biology/py-orange3-bioinformatics: Update 3.1.1 -> 3.2.0 2018-08-09 00:29:50 +00:00
py-orange3-single-cell biology/py-orange3-single-cell: Update 0.7.0 -> 0.8.0 2018-08-08 23:08:51 +00:00
py-pysam biology/py-pysam: Update 0.14.1 -> 0.15.0 2018-07-30 19:47:49 +00:00
pycogent Use PY_FLAVOR for dependencies. 2018-06-20 17:05:41 +00:00
pyfasta Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
python-nexus - Update to 1.61 2018-04-01 11:52:08 +00:00
rainbow biology/rainbow: Efficient clustering and assembling of short reads 2018-04-02 16:50:46 +00:00
recombine
ruby-bio - Update to 1.5.1 2017-05-07 15:44:34 +00:00
rubygem-bio Update to 1.5.1 2017-02-06 23:03:17 +00:00
samtools biology/samtools: update to 1.9 2018-08-02 19:28:36 +00:00
seaview biology/seaview: Updatye version 4.6.5=>4.7 2018-07-22 03:22:15 +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 1.68.0 2018-08-09 06:58:30 +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 biology/seqtools: re-try on powerpc* after r449590 2017-12-12 03:38:56 +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 2018-07-29 22:18:44 +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 2018-07-29 22:18:44 +00:00
tabixpp biology/tabixpp: C++ wrapper to tabix indexer 2018-04-14 23:52:16 +00:00
tinker Bump PORTREVISION for ports depending on the canonical version of GCC 2018-07-29 22:18:44 +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 Mark BROKEN: missing plist 2018-06-29 12:43:19 +00:00
ugene Replace bsd.qt.mk by Uses/qt.mk and Uses/qt-dist.mk 2018-06-28 17:39:53 +00:00
unanimity devel/boost-*: update to 1.68.0 2018-08-09 06:58:30 +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 Remove libintl.so.9 compatibility link that was added in r374303 to 2016-12-08 19:52:19 +00:00
xmolwt Remove libintl.so.9 compatibility link that was added in r374303 to 2016-12-08 19:52:19 +00:00
Makefile Remove expired ports: 2018-08-16 20:28:32 +00:00