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efc62e6bcd
freebsd-ports/biology
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Mark Linimon efc62e6bcd Adjust USES to fix builds on gcc-based architectures. 
While here, pet portlint.

Tested for no regression on amd64.

Approved by:	portmgr (tier-2 blanket)
2018-06-18 19:03:03 +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 Add a USES=python:env, that will not add a dependency on Python. 2017-12-04 15:27:29 +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
blat - Update WWW 2017-06-10 09:01:19 +00:00
bowtie Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +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 biology/canu: Upgrade to 1.7 release 2018-04-26 04:16:15 +00:00
cd-hit Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
cdbfasta Multiple ports: 2018-01-31 01:07:07 +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 biology/clustalx: Multiple alignment of nucleic acid and protein sequences with GUI 2018-05-21 20:56:17 +00:00
consed
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
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 Mark the latest version broken on armvX. Note: 2.1.8.3 built ok. 2018-03-18 13:38:23 +00:00
fastx-toolkit biology/fastx-toolkit: Fix build on FreeBSD 12 2018-05-16 15:13:43 +00:00
fluctuate
freebayes biology/freebayes: Bayesian haplotype-based polymorphism discovery and genotyping 2018-04-20 00:07:27 +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
grappa
hmmer Back out previous commits by jbeich demand. 2017-12-18 04:28:28 +00:00
htslib biology/htslib biology/bcftools biology/samtools: Update to 1.6 2017-10-25 10:19:50 +00:00
hyphy biology/hyphy: Update to version 2.3.13 2018-05-22 22:55:18 +00:00
infernal Add new port: biology/infernal 2018-06-06 15:15:18 +00:00
iolib
iqtree Mark ports broken on powerpc64, categories a-c. 2018-06-18 01:48:46 +00:00
jalview
jellyfish Multiple ports: 2018-01-31 01:07:07 +00:00
kallisto Adjust USES to fix building on gcc-based archs (in particular, powerpc64). 2018-06-02 19:40:59 +00:00
lagan
lamarc
libgtextutils biology/libgtextutils: Unbreak for FreeBSD 12 2018-03-29 15:41:07 +00:00
libsbml - Update to 5.16.0 2018-01-01 08:24:53 +00:00
linux-foldingathome
mafft
mapm3
migrate Mark broken on armvX and mips. 2018-03-18 13:48:07 +00:00
molden biolog/molden: unbreak after at least two intransparent distfile updates 2018-05-20 21:41:57 +00:00
mopac Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +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+ Mark as broken on powerpc64. The entire, unhelpful, error message is: 2018-06-03 11:14:53 +00:00
ncbi-toolkit
ngs-sdk New port: biology/ngs-sdk: Tools and libraries for using data in the INSDC Sequence Read Archives 2018-06-10 23:58:07 +00:00
njplot
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 biology/pbbam: PacBio BAM C++ library, with SWIG bindings 2018-04-23 16:08:21 +00:00
pbcopper biology/pbcopper: Core C++ library for Pacific Biosciences tools 2018-04-23 16:23:53 +00:00
pbseqan biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn 2018-04-21 17:21:30 +00:00
pear-merger biology/pear-merger: Memory-efficient and accurate paired-end read merger 2018-04-04 17:21:39 +00:00
phrap
phred
phylip - Update to 3.697 2018-01-01 08:40:22 +00:00
phyml - Update to 3.3.20180214 2018-05-15 03:17:54 +00:00
plinkseq Multiple ports: 2018-01-31 01:07:07 +00:00
primer3
protomol
psi88 Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-biom-format Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-biopython biology/py-biopython: Unbreak on python3; Add license 2018-05-13 22:30:00 +00:00
py-bx-python Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
py-cutadapt Switch all pypi.python.org WWWs to a new PyPi home pypi.org where 2018-04-25 16:42:37 +00:00
py-Genesis-PyAPI biology/py-Genesis-PyAPI: Remove stray USES=fortran 2018-06-13 01:48:40 +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 New port: biology/py-orange3-bioinformatics: Orange add-on providing common functionality for bioinformatics 2018-06-14 06:25:21 +00:00
py-pysam Switch all pypi.python.org WWWs to a new PyPi home pypi.org where 2018-04-25 16:42:37 +00:00
pycogent Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +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
rubygem-bio
samtools Add a USES=python:env, that will not add a dependency on Python. 2017-12-04 15:27:29 +00:00
seaview biology/seaview: Update version 4.6.3=>4.6.5 2018-04-24 12:31:32 +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 1.67.0 2018-04-18 13:57:42 +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 Adjust USES to fix builds on gcc-based architectures. 2018-06-18 19:03:03 +00:00
t_coffee Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
tabixpp biology/tabixpp: C++ wrapper to tabix indexer 2018-04-14 23:52:16 +00:00
tinker Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
treepuzzle
trimadap biology/trimadap: Trim adapter sequences from Illumina data 2018-04-03 18:23:54 +00:00
trimmomatic Multiple ports: 2018-01-31 01:07:07 +00:00
tRNAscan-SE Update to 2.0.0 and pass maintainership to committer. 2018-06-06 15:20:57 +00:00
ugene Add upstream patch to fix the build with Qt 5.10. 2018-05-15 18:51:51 +00:00
unanimity biology/unanimity: Pacific Biosciences consensus library and applications 2018-04-24 14:16:46 +00:00
vcflib biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF files 2018-04-17 03:11:39 +00:00
vcftools Multiple ports: 2018-01-31 01:07:07 +00:00
velvet - Convert to option helper install target (add OPTIONS_DEFINE=DOCS 2018-01-11 18:09:00 +00:00
wise
xmolwt
Makefile New port: biology/py-orange3-bioinformatics: Orange add-on providing common functionality for bioinformatics 2018-06-14 06:25:21 +00:00