| .. |
|
abyss
|
biology/abyss: Update 2.2.4 -> 2.2.5
|
2020-09-27 06:59:05 +00:00 |
|
artemis
|
|
|
|
avida
|
For ports on riscv64 that fail the same (or similar ways) to aarch64, mark
|
2021-01-02 01:46:08 +00:00 |
|
babel
|
|
|
|
bamtools
|
Bump devel/jsoncpp consumers after r540853.
|
2020-06-30 17:46:18 +00:00 |
|
bcftools
|
biology/bcftools: Upgrade to 1.11
|
2020-11-05 20:34:03 +00:00 |
|
bedtools
|
biology/bedtools: Upgrade to 2.30.0
|
2021-01-24 18:25:39 +00:00 |
|
bioawk
|
biology/bioawk: BWK awk modified for biological data
|
2020-06-05 02:45:33 +00:00 |
|
biococoa
|
Return theraven's ports to the pool after safekeeping his commit bit.
|
2020-03-05 20:49:05 +00:00 |
|
bioparser
|
biology/bioparser: Cosmetic changes
|
2021-01-19 09:56:15 +00:00 |
|
biosoup
|
New port: biology/biosoup: Collection of C++ header-only data structures for bioinformatics
|
2021-01-19 09:01:41 +00:00 |
|
bolt-lmm
|
Canonicalize powerpc64le CXXFLAGS to be the same as powerpc64.
|
2020-09-27 07:41:33 +00:00 |
|
bowtie
|
biology/bowtie: Unbreak build with GCC 10
|
2020-07-04 10:46:08 +00:00 |
|
bowtie2
|
biology/bowtie2: Upgrade to 2.4.2
|
2020-11-07 13:47:41 +00:00 |
|
bwa
|
For ports on riscv64 that fail the same (or similar ways) to aarch64, mark
|
2021-01-02 01:46:08 +00:00 |
|
canu
|
biology/canu: Drop dependency on gcc
|
2021-01-11 16:51:15 +00:00 |
|
cd-hit
|
biology/cd-hit: Drop dependency on gcc
|
2021-01-11 16:55:15 +00:00 |
|
cdbfasta
|
|
|
|
checkm
|
scipy 1.5.4 is only compatible with python 3.6+
|
2020-12-24 09:03:39 +00:00 |
|
clustal-omega
|
|
|
|
clustalw
|
|
|
|
cufflinks
|
- Upgrade math/eigen3 to 3.3.8;
|
2020-12-12 17:04:37 +00:00 |
|
cytoscape
|
|
|
|
ddocent
|
|
|
|
diamond
|
biology/diamond: Update to version 2.0.6
|
2020-12-20 20:21:41 +00:00 |
|
dsr-pdb
|
|
|
|
edlib
|
Fix build on GCC-based systems by adding compiler:c++14-lang to USES:
|
2021-01-20 02:31:33 +00:00 |
|
emboss
|
- update libgd to 2.3.0
|
2020-05-04 21:31:39 +00:00 |
|
exonerate
|
|
|
|
fasta
|
|
|
|
fasta3
|
|
|
|
fastahack
|
|
|
|
fastdnaml
|
|
|
|
fastool
|
|
|
|
fastp
|
biology/fastp: Upgrade to 0.20.1
|
2020-04-09 16:17:02 +00:00 |
|
fastqc
|
|
|
|
fasttree
|
biology/fasttree: Drop dependency on gcc
|
2021-01-11 16:58:13 +00:00 |
|
fastx-toolkit
|
|
|
|
figtree
|
Add education virtual category
|
2020-11-20 07:16:06 +00:00 |
|
fluctuate
|
|
|
|
freebayes
|
For ports on riscv64 that fail the same (or similar ways) to aarch64, mark
|
2021-01-02 01:46:08 +00:00 |
|
garlic
|
|
|
|
gatk
|
biology/gatk: Add the WITH_LARGE_FILES option.
|
2021-01-22 02:50:38 +00:00 |
|
gcta
|
biology/gcta: Drop dependency on gcc
|
2021-01-11 17:09:37 +00:00 |
|
gemma
|
biology/gemma: Upgrade to 0.98.3
|
2021-01-02 22:05:58 +00:00 |
|
gff2ps
|
|
|
|
gmap
|
biology/gmap: enable on powerpc64le
|
2020-10-09 13:23:12 +00:00 |
|
gperiodic
|
- Update WWW
|
2020-01-19 09:30:22 +00:00 |
|
graphlan
|
biology/graphlan: Remove the 2.7 limitation on python because it's no longer needed
|
2020-08-14 04:59:29 +00:00 |
|
grappa
|
Extend expiration of ports broken with -fno-common
|
2020-08-30 09:47:49 +00:00 |
|
groopm
|
scipy 1.5.4 is only compatible with python 3.6+
|
2020-12-24 09:03:39 +00:00 |
|
haplohseq
|
biology/haplohseq: Fix example scripts for python 3
|
2021-01-23 19:31:49 +00:00 |
|
hhsuite
|
biology/hhsuite: Update 3.2.0 -> 3.3.0
|
2020-08-27 04:28:24 +00:00 |
|
hisat2
|
|
|
|
hmmer
|
Also enable on powerpc64le.
|
2020-09-24 20:29:35 +00:00 |
|
htslib
|
biology/htslib: Upgrade to 1.11.0
|
2020-11-05 20:30:50 +00:00 |
|
hyphy
|
biology/hyphy: Update to version 2.5.27
|
2021-01-27 11:33:53 +00:00 |
|
igv
|
biology/igv: Fix fetch by fixing a small left-over mistake
|
2020-11-30 17:29:48 +00:00 |
|
infernal
|
Also enable on powerpc64le.
|
2020-09-24 20:38:59 +00:00 |
|
iolib
|
|
|
|
iqtree
|
biology/iqtree: Remove USES=compiler:openmp, fix amd64 clang++ build
|
2021-01-12 18:12:12 +00:00 |
|
jalview
|
Restrict to Java 8, since this doesn't compile with Java 11
|
2020-12-26 23:01:20 +00:00 |
|
jellyfish
|
biology/htslib: Upgrade to 1.10.2
|
2020-08-03 17:40:04 +00:00 |
|
kallisto
|
biology/kallisto: Add -lz for pending hdf5 upgrade
|
2021-01-26 01:34:20 +00:00 |
|
lagan
|
Extend expiration of ports broken with -fno-common
|
2020-08-30 09:47:49 +00:00 |
|
lamarc
|
|
|
|
libbigwig
|
|
|
|
libgtextutils
|
|
|
|
libsbml
|
Set CMAKE options explicitly
|
2020-12-20 15:23:50 +00:00 |
|
linux-foldingathome
|
Update to 7.6.13
|
2020-05-09 13:21:29 +00:00 |
|
mafft
|
|
|
|
mapm3
|
biology/mapm3: Reformat patches.
|
2020-09-04 12:24:23 +00:00 |
|
migrate
|
Mark BROKEN on riscv64 the same as armv*:
|
2021-01-19 02:26:53 +00:00 |
|
minimap2
|
|
|
|
molden
|
|
|
|
mopac
|
|
|
|
mothur
|
biology/mothur: fix build on powerpc64le
|
2020-10-19 10:30:11 +00:00 |
|
mrbayes
|
- Swap back from net/openmpi3 to net/openmpi
|
2020-04-21 21:47:57 +00:00 |
|
mummer
|
biology/mummer: fix build on powerpc64 elfv2 and powerpc64le
|
2020-10-25 23:03:14 +00:00 |
|
muscle
|
|
|
|
ncbi-blast+
|
biology/ncbi-blast+: Drop dependency on gcc
|
2021-01-11 17:17:35 +00:00 |
|
ncbi-cxx-toolkit
|
biology/ncbi-cxx-toolkit: Fix build on 13
|
2020-09-27 04:57:44 +00:00 |
|
ncbi-toolkit
|
Chase security/p11-kit update
|
2020-08-30 03:10:23 +00:00 |
|
ngs-sdk
|
For ports on riscv64 that fail the same (or similar ways) to aarch64, mark
|
2021-01-02 01:46:08 +00:00 |
|
p5-AcePerl
|
|
|
|
p5-Bio-ASN1-EntrezGene
|
|
|
|
p5-Bio-Cluster
|
|
|
|
p5-Bio-Coordinate
|
Cosmetic change
|
2020-04-02 12:01:30 +00:00 |
|
p5-Bio-Das
|
|
|
|
p5-Bio-Das-Lite
|
|
|
|
p5-Bio-DB-EMBL
|
|
|
|
p5-Bio-DB-NCBIHelper
|
|
|
|
p5-Bio-FeatureIO
|
Cosmetic change
|
2020-04-02 12:01:35 +00:00 |
|
p5-Bio-GFF3
|
|
|
|
p5-Bio-Glite
|
|
|
|
p5-Bio-Graphics
|
|
|
|
p5-Bio-MAGETAB
|
|
|
|
p5-Bio-NEXUS
|
|
|
|
p5-Bio-Phylo
|
|
|
|
p5-Bio-SCF
|
|
|
|
p5-Bio-Variation
|
|
|
|
p5-BioPerl
|
Move devel/p5-IO-stringy to devel/p5-IO-Stringy and update to 2.113
|
2020-06-26 11:55:23 +00:00 |
|
p5-BioPerl-Run
|
|
|
|
p5-transdecoder
|
|
|
|
p5-TrimGalore
|
|
|
|
paml
|
biology/paml: fix the build with LLVM 11
|
2020-08-20 17:07:03 +00:00 |
|
pbbam
|
biology/htslib: Upgrade to 1.10.2
|
2020-08-03 17:40:04 +00:00 |
|
pbseqan
|
|
|
|
pear-merger
|
For ports on riscv64 that fail the same (or similar ways) to aarch64, mark
|
2021-01-02 01:46:08 +00:00 |
|
phrap
|
Sanitize COMMENT per Section 5.6 of the FreeBSD Porter's Handbook (part 1).
|
2020-05-27 11:59:13 +00:00 |
|
phred
|
|
|
|
phylip
|
Extend expiration of ports broken with -fno-common
|
2020-08-30 09:47:49 +00:00 |
|
phyml
|
biology/phyml: fix build on recent current
|
2020-08-29 08:34:27 +00:00 |
|
picard-tools
|
biology/picard-tools: Remove extraneous file
|
2020-08-30 14:06:54 +00:00 |
|
plink
|
Allow building on powerpc64le.
|
2020-09-27 07:44:15 +00:00 |
|
pooler
|
biology/pooler: Upgrade to 1.76
|
2021-01-08 22:44:13 +00:00 |
|
primer3
|
|
|
|
prodigal
|
|
|
|
prodigy-lig
|
Unbreak bulk -a
|
2020-06-13 15:05:44 +00:00 |
|
protomol
|
|
|
|
psi88
|
biology/psi88: Unbreak build with GCC 10
|
2020-07-04 12:15:58 +00:00 |
|
py-biom-format
|
biology/py-biom-format: Update to version 2.1.10
|
2021-01-11 05:28:11 +00:00 |
|
py-biopython
|
biology/py-biopython: Upgrade to 1.78
|
2020-10-16 19:12:43 +00:00 |
|
py-bx-python
|
Drop python 2.7 support from a few ports
|
2020-12-28 23:02:12 +00:00 |
|
py-cutadapt
|
|
|
|
py-dnaio
|
biology/py-dnaio: Upgrade to 0.4.2
|
2020-05-24 15:23:15 +00:00 |
|
py-ete3
|
Update PyQt5 to 5.15.2, sip to 5.5.0, py-qtbuilder to 1.6.0 and py-qt5-sip to 12.8.1
|
2020-12-15 17:56:00 +00:00 |
|
py-fastTSNE
|
Drop dependency on devel/openmp
|
2020-03-08 21:56:36 +00:00 |
|
py-Genesis-PyAPI
|
Drop python 2.7 support from a few ports
|
2020-12-28 23:02:12 +00:00 |
|
py-gffutils
|
Unbreak bulk -a
|
2020-07-14 07:59:28 +00:00 |
|
py-gtfparse
|
Drop python 2.7 support from a few ports
|
2020-12-28 23:02:12 +00:00 |
|
py-hits
|
New port: biology/py-hits: Utilities for processing high-throughput sequencing experiments
|
2020-05-16 03:11:05 +00:00 |
|
py-loompy
|
biology/py-loompy: Update 2.0.17 -> 3.0.6
|
2020-06-16 02:26:08 +00:00 |
|
py-macs2
|
biology/py-macs2: Upgrade to 2.2.7.1
|
2020-04-14 12:13:55 +00:00 |
|
py-multiqc
|
Unbreak bulk -a
|
2020-09-19 14:15:42 +00:00 |
|
py-orange3-bioinformatics
|
|
|
|
py-orange3-single-cell
|
Remove PY_SPHINX from ports using Python 3
|
2021-01-14 14:34:38 +00:00 |
|
py-pandas-charm
|
Drop python 2.7 support from a few ports
|
2020-12-28 23:02:12 +00:00 |
|
py-pyfaidx
|
Drop python 2.7 support from a few ports
|
2020-12-28 23:02:12 +00:00 |
|
py-pysam
|
Drop python 2.7 support from a few ports
|
2020-12-28 23:02:12 +00:00 |
|
py-scikit-bio
|
Add education virtual category
|
2020-11-20 07:16:06 +00:00 |
|
py-xenaPython
|
Drop python 2.7 support from a few ports
|
2020-12-28 23:02:12 +00:00 |
|
pyfasta
|
Drop python 2.7 support from a few ports
|
2020-12-28 23:02:12 +00:00 |
|
python-nexus
|
Drop python 2.7 support from a few ports
|
2020-12-28 23:02:12 +00:00 |
|
rainbow
|
Update WWW
|
2020-03-31 23:18:09 +00:00 |
|
rampler
|
Add compiler:c++11-lang to USES to fix build on GCC-based systems:
|
2021-01-20 02:30:13 +00:00 |
|
recombine
|
|
|
|
ruby-bio
|
biology/ruby-bio: remove expired optional dependency on textproc/ruby-xmlparser
|
2020-05-05 14:22:09 +00:00 |
|
rubygem-bio
|
Update to 2.0.1
|
2020-07-24 07:49:43 +00:00 |
|
rubygem-bio-executables
|
Add rubygem-bio-executables 1.0.0
|
2020-07-24 07:08:00 +00:00 |
|
rubygem-bio-old-biofetch-emulator
|
Add rubygem-bio-old-biofetch-emulator 1.0.0
|
2020-07-24 07:08:05 +00:00 |
|
rubygem-bio-shell
|
Add rubygem-bio-shell 1.0.0
|
2020-07-24 07:08:11 +00:00 |
|
samtools
|
biology/samtools: Upgrade to 1.11
|
2020-11-05 20:32:39 +00:00 |
|
scrm
|
Add compiler:c++11-lang to USES to fix build on GCC-based systems:
|
2020-05-15 07:30:34 +00:00 |
|
seaview
|
biology/seaview: Update version 5.0.3=>5.0.4
|
2020-06-22 17:34:44 +00:00 |
|
seqan
|
|
|
|
seqan1
|
|
|
|
seqan-apps
|
|
|
|
seqio
|
|
|
|
seqtk
|
|
|
|
sim4
|
|
|
|
slclust
|
|
|
|
smithwaterman
|
|
|
|
spoa
|
New port: biology/spoa: C++ implementation of the partial order alignment (POA) algorithm
|
2021-01-19 09:28:00 +00:00 |
|
stacks
|
biology/stacks: Drop dependency on gcc
|
2021-01-11 17:27:30 +00:00 |
|
star
|
biology/star: Drop dependency on gcc
|
2021-01-11 17:39:52 +00:00 |
|
stringtie
|
biology/stringtie: fix build on GCC architectures
|
2020-02-23 10:52:44 +00:00 |
|
subread
|
biology/subread: Add -fcommon for clang 11
|
2020-09-18 00:57:35 +00:00 |
|
tabixpp
|
biology/tabixpp: fix build on GCC architectures
|
2020-11-23 16:13:15 +00:00 |
|
treekin
|
Fix math/openblas and bump dependent ports
|
2020-01-30 14:17:44 +00:00 |
|
treepuzzle
|
|
|
|
trimadap
|
|
|
|
trimmomatic
|
|
|
|
tRNAscan-SE
|
|
|
|
ugene
|
Mark BROKEN on riscv64 the same as on aarch64.
|
2021-01-19 02:29:16 +00:00 |
|
vcflib
|
For ports on riscv64 that fail the same (or similar ways) to aarch64, mark
|
2021-01-02 01:46:08 +00:00 |
|
vcftools
|
|
|
|
velvet
|
|
|
|
viennarna
|
biology/viennarna: Update 2.4.16 -> 2.4.17
|
2020-12-06 20:14:53 +00:00 |
|
vsearch
|
biology/vsearch: enable on powerpc64le
|
2021-01-16 17:51:56 +00:00 |
|
vt
|
biology/vt: Fix build with htslib 1.11
|
2020-11-09 00:35:58 +00:00 |
|
wise
|
|
|
|
Makefile
|
New port: biology/rampler: Standalone module for sampling genomic sequences
|
2021-01-19 09:49:53 +00:00 |
