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freebsd-ports/biology
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Joseph Mingrone 94e4c0f0fb biology/diamond: Update to version 0.9.18-49 
Pull in commits after the 0.9.18 release for build fixes.

Upstream changes: https://github.com/bbuchfink/diamond/releases/tag/v0.9.18
2018-03-15 02:28:09 +00:00
..
ariadne
Mark as broken ports with no public distfiles
2017-10-13 11:14:53 +00:00
artemis
Remove dead master sites
2017-10-13 11:14:32 +00:00
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
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 0.9.18-49
2018-03-15 02:28:09 +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
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +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
biology/htslib biology/bcftools biology/samtools: Update to 1.6
2017-10-25 10:19:50 +00:00
iolib
…
iqtree
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
jalview
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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
Multiple ports:
2018-01-31 01:07:07 +00:00
libsbml
- Update to 5.16.0
2018-01-01 08:24:53 +00:00
linux-foldingathome
…
mafft
…
mapm3
…
migrate
…
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
- Fix installing scripts and support binaries
2017-10-30 02:27:23 +00:00
muscle
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ncbi-blast+
Bump PORTREVISIONs of all users of math/mpc that we just updated to
2018-03-10 17:46:04 +00:00
ncbi-toolkit
…
njplot
…
p5-AcePerl
Fix license information for portgs that use "the same license as Perl".
2017-09-15 08:58:46 +00:00
p5-Bio-ASN1-EntrezGene
Fix license information for portgs that use "the same license as Perl".
2017-09-15 08:58:46 +00:00
p5-Bio-Coordinate
Fix license information for portgs that use "the same license as Perl".
2017-09-15 08:58:46 +00:00
p5-Bio-Das
Fix license information for portgs that use "the same license as Perl".
2017-09-15 08:58:46 +00:00
p5-Bio-Das-Lite
Fix license information for portgs that use "the same license as Perl".
2017-09-15 08:58:46 +00:00
p5-Bio-FeatureIO
Add p5-Bio-FeatureIO 1.6.905
2017-09-15 19:17:17 +00:00
p5-Bio-GFF3
Fix license information for portgs that use "the same license as Perl".
2017-09-15 08:58:46 +00:00
p5-Bio-Glite
…
p5-Bio-Graphics
Fix license information for portgs that use "the same license as Perl".
2017-09-15 08:58:46 +00:00
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
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
…
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
2018-02-10 23:01:37 +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
Convert Python ports to FLAVORS.
2017-11-30 15:50:30 +00:00
recombine
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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
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
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trimmomatic
Multiple ports:
2018-01-31 01:07:07 +00:00
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
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
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xmolwt
…
Makefile
[new port] biology/canu: Single molecule sequence assembler
2017-12-22 01:30:26 +00:00