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freebsd-ports/biology
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Jason W. Bacon 56d5a1146f biology/stacks: Software pipeline for building loci from short-read sequences 
Reviewed by:    mat
Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D14885
2018-03-31 13:16:05 +00:00
..
ariadne
artemis
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 - Fix build on 11+ 2017-12-22 12:27:14 +00:00
biococoa Fix configure options for gnustep-make 2017-12-03 12:23:53 +00:00
blat
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 Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +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
clustalw
consed
crux Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
diamond biology/diamond: Update to version 0.9.19 2018-03-17 15:29:13 +00:00
emboss
fasta
fasta3
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 Multiple ports: 2018-01-31 01:07:07 +00:00
fluctuate
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
iolib
iqtree biology/iqtree: Update to version 1.6.3 2018-03-23 01:22:47 +00:00
jalview
jellyfish Multiple ports: 2018-01-31 01:07:07 +00:00
kallisto [new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq data 2017-12-02 20:44:28 +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 Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +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
mummer
muscle
ncbi-blast+ biology/ncbi-blast+: Upgrade to 2.7.1 2018-03-27 18:04:21 +00:00
ncbi-toolkit
njplot
p5-AcePerl
p5-Bio-ASN1-EntrezGene
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 Update to 2.0.1 2017-12-26 23:20:28 +00:00
p5-Bio-SCF
p5-BioPerl
p5-BioPerl-Run
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
phrap
phred
phylip - Update to 3.697 2018-01-01 08:40:22 +00:00
phyml Remove now-useless, commented-out lines. 2018-03-10 23:35:03 +00:00
plink Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +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 Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +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 Canonicalize PyPi WWWs: 2018-02-08 20:18:08 +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-pysam biology/py-pysam: Update to 0.14.1 2018-03-21 08:12:32 +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 Convert Python ports to FLAVORS. 2017-11-30 15:50:30 +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 4.6.2=>4.6.3 2018-01-05 17:40:41 +00:00
seqan biology/seqan-apps, biology/seqan: Update to 2.4.0 2018-03-10 06:21:37 +00:00
seqan1
seqan-apps biology/seqan-apps, biology/seqan: Update to 2.4.0 2018-03-10 06:21:37 +00:00
seqio - Switch to options helpers 2017-11-26 09:00:21 +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
ssaha Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
stacks biology/stacks: Software pipeline for building loci from short-read sequences 2018-03-31 13:16:05 +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
tinker Bump PORTREVISIONs of all users of math/mpc that we just updated to 2018-03-10 17:46:04 +00:00
treepuzzle
trimmomatic Multiple ports: 2018-01-31 01:07:07 +00:00
tRNAscan-SE
ugene Update Qt5 ports to 5.9.3. 2018-01-06 21:30:31 +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 biology/stacks: Software pipeline for building loci from short-read sequences 2018-03-31 13:16:05 +00:00