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freebsd-ports/biology
History
Alexey Dokuchaev 35f74fbe2e - Convert to option helper install target (add OPTIONS_DEFINE=DOCS 
when it was missing)
- Invoke INSTALL_DATA where appropriate instead of INSTALL_MAN
- Fix some whitespace and formatting bugs along the way
2018-01-11 18:09:00 +00:00
..
ariadne
Mark as broken ports with no public distfiles
2017-10-13 11:14:53 +00:00
artemis
…
avida
Try to bring some consistency to ports that have x86-specific pieces.
2017-12-21 10:23:19 +00:00
babel
…
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
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bowtie2
biology/bowtie2: Upgrade to 2.3.3.1
2017-11-30 02:59:16 +00:00
bwa
[unbreak] biology/bwa: Remove old patch files
2017-12-01 02:42:54 +00:00
canu
biology/canu: Replace += with = for depends
2017-12-22 14:14:11 +00:00
cd-hit
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cdbfasta
…
chemeq
…
clustalw
…
consed
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crux
For ports that are marked BROKEN on armv6, and also fail to build on
2017-11-30 06:13:34 +00:00
diamond
biology/diamond: Update to version 0.9.14
2017-12-13 16:31:53 +00:00
emboss
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fasta
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fasta3
…
fastdnaml
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fastool
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fastqc
[new port] biology/fastqc: Quality control tool for high throughput sequence data
2017-11-30 22:54:29 +00:00
fasttree
biology/fasttree: update to version 2.1.10
2017-12-05 03:03:38 +00:00
fastx-toolkit
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fluctuate
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garlic
…
gff2ps
…
gmap
Try to bring some consistency to ports that have x86-specific pieces.
2017-12-21 10:23:19 +00:00
gperiodic
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grappa
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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
iolib
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iqtree
New USES=eigen
2018-01-02 16:49:24 +00:00
jalview
…
jellyfish
…
kallisto
[new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq data
2017-12-02 20:44:28 +00:00
lagan
…
lamarc
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libgtextutils
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libsbml
- Update to 5.16.0
2018-01-01 08:24:53 +00:00
linux-foldingathome
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mafft
…
mapm3
…
migrate
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molden
biology/molden: chase another intransparent upstream distfile upgrade.
2017-11-01 03:48:30 +00:00
mopac
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mrbayes
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mummer
- Fix installing scripts and support binaries
2017-10-30 02:27:23 +00:00
muscle
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ncbi-blast+
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ncbi-toolkit
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njplot
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p5-AcePerl
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p5-Bio-ASN1-EntrezGene
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p5-Bio-Coordinate
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p5-Bio-Das
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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
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p5-BioPerl
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p5-BioPerl-Run
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p5-transdecoder
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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
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phrap
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phred
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phylip
- Update to 3.697
2018-01-01 08:40:22 +00:00
phyml
Disable the extra flag "-march=native" on arm to fix builds.
2017-12-27 07:36:05 +00:00
plink
Mark as broken ports with no public distfiles
2017-10-13 11:14:53 +00:00
plinkseq
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primer3
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protomol
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psi88
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py-biom-format
biology/py-biom-format: Add required dependency on math/py-pandas and do
2017-12-10 03:33:04 +00:00
py-biopython
Convert Python ports to FLAVORS.
2017-11-30 15:50:30 +00:00
py-bx-python
Convert Python ports to FLAVORS.
2017-11-30 15:50:30 +00:00
py-cutadapt
Fix packaging with python3
2017-12-01 06:18:17 +00:00
py-macs2
biology/py-macs2: Restrict to python 2.7.
2017-12-05 02:59:01 +00:00
py-pysam
Convert Python ports to FLAVORS.
2017-11-30 15:50:30 +00:00
pycogent
- Those ports fail to build with python3
2017-12-11 16:54:20 +00:00
pyfasta
Convert Python ports to FLAVORS.
2017-11-30 15:50:30 +00:00
python-nexus
Convert Python ports to FLAVORS.
2017-11-30 15:50:30 +00:00
recombine
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ruby-bio
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rubygem-bio
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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
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seqan1
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seqan-apps
Mark several ports newly broken on arm.
2017-12-11 07:18:48 +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
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slclust
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ssaha
Mark as broken ports with no public distfiles
2017-10-13 11:14:53 +00:00
t_coffee
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tinker
Fix the context of some patches so that they apply with stricter patch(1)
2017-11-09 20:45:04 +00:00
treepuzzle
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trimmomatic
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tRNAscan-SE
Mark as broken ports with no public distfiles
2017-10-13 11:14:53 +00:00
ugene
Update Qt5 ports to 5.9.3.
2018-01-06 21:30:31 +00:00
vcftools
biology/vcftools: Upgrade to latest release 0.1.15
2017-11-27 23:05:40 +00:00
velvet
- Convert to option helper install target (add OPTIONS_DEFINE=DOCS
2018-01-11 18:09:00 +00:00
wise
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xmolwt
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Makefile
[new port] biology/canu: Single molecule sequence assembler
2017-12-22 01:30:26 +00:00