| .. |
|
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 PORTREVISION for ports depending on the canonical version of GCC
|
2017-09-10 20:55:38 +00:00 |
|
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
|
devel/boost-*: update to 1.66.0
|
2018-01-18 04:11:02 +00:00 |
|
cd-hit
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2017-09-10 20:55:38 +00:00 |
|
cdbfasta
|
|
|
|
chemeq
|
|
|
|
clustalw
|
|
|
|
consed
|
|
|
|
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
|
|
|
|
fasta
|
|
|
|
fasta3
|
|
|
|
fastdnaml
|
|
|
|
fastool
|
|
|
|
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
|
|
|
|
fluctuate
|
|
|
|
garlic
|
|
|
|
gff2ps
|
|
|
|
gmap
|
Try to bring some consistency to ports that have x86-specific pieces.
|
2017-12-21 10:23:19 +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
|
New USES=eigen
|
2018-01-02 16:49:24 +00:00 |
|
jalview
|
|
|
|
jellyfish
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2017-09-10 20:55:38 +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
|
|
|
|
libsbml
|
- Update to 5.16.0
|
2018-01-01 08:24:53 +00:00 |
|
linux-foldingathome
|
|
|
|
mafft
|
|
|
|
mapm3
|
|
|
|
migrate
|
|
|
|
molden
|
biology/molden: chase another intransparent upstream distfile upgrade.
|
2017-11-01 03:48:30 +00:00 |
|
mopac
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2017-09-10 20:55:38 +00:00 |
|
mrbayes
|
|
|
|
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
|
2017-09-10 20:55:38 +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
|
|
|
|
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
|
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
|
|
|
|
primer3
|
|
|
|
protomol
|
|
|
|
psi88
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2017-09-10 20:55:38 +00:00 |
|
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
|
|
|
|
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
|
|
|
|
seqan1
|
|
|
|
seqan-apps
|
devel/boost-*: update to 1.66.0
|
2018-01-18 04:11:02 +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
|
|
|
|
ssaha
|
Mark as broken ports with no public distfiles
|
2017-10-13 11:14:53 +00:00 |
|
t_coffee
|
Bump PORTREVISION for ports depending on the canonical version of GCC
|
2017-09-10 20:55:38 +00:00 |
|
tinker
|
Fix the context of some patches so that they apply with stricter patch(1)
|
2017-11-09 20:45:04 +00:00 |
|
treepuzzle
|
|
|
|
trimmomatic
|
|
|
|
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
|
|
|
|
xmolwt
|
|
|
|
Makefile
|
[new port] biology/canu: Single molecule sequence assembler
|
2017-12-22 01:30:26 +00:00 |
25beeff079