..
abyss
biology/abyss: Update 2.2.4 -> 2.2.5
2020-09-27 06:59:05 +00:00
artemis
avida
babel
bamtools
Bump devel/jsoncpp consumers after r540853.
2020-06-30 17:46:18 +00:00
bcftools
biology/bcftools: Upgrade to 1.10.2
2020-08-03 18:16:54 +00:00
bedtools
bioawk
biology/bioawk: BWK awk modified for biological data
2020-06-05 02:45:33 +00:00
biococoa
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
Update devel/tbb to 2020.3 and bump dependent ports' revisions
2020-07-17 10:12:25 +00:00
bwa
biology/bwa: fix build on recent current
2020-08-28 11:17:13 +00:00
canu
biology/canu: Upgrade to 2.1
2020-09-14 22:27:37 +00:00
cd-hit
cdbfasta
checkm
clustal-omega
clustalw
cufflinks
biology/cufflinks: fix build on recent current
2020-08-28 18:24:04 +00:00
cytoscape
ddocent
diamond
biology/diamond: Update to version 2.0.4
2020-08-30 16:14:22 +00:00
dsr-pdb
emboss
exonerate
fasta
fasta3
fastahack
fastdnaml
fastool
fastp
fastqc
fasttree
fastx-toolkit
figtree
fluctuate
freebayes
Fix build with -fno-common
2020-09-21 18:14:57 +00:00
garlic
gatk
biology/gatk: Fix build
2020-09-08 19:25:36 +00:00
gcta
gemma
gff2ps
gmap
biology/gmap: enable on powerpc64le
2020-10-09 13:23:12 +00:00
gperiodic
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
biology/groopm: Remove python's 2.7 restriction placed here by mistake
2020-08-13 19:19:23 +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 1.10.2
2020-08-03 17:40:04 +00:00
hyphy
biology/hyphy: Update to version 2.5.20
2020-10-16 23:43:17 +00:00
igv
infernal
Also enable on powerpc64le.
2020-09-24 20:38:59 +00:00
iolib
iqtree
jalview
jellyfish
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
kallisto
biology/kallisto: Revert to 0.46.1
2020-08-03 15:45:21 +00:00
lagan
Extend expiration of ports broken with -fno-common
2020-08-30 09:47:49 +00:00
lamarc
libbigwig
libgtextutils
libsbml
Convert REINPLACE_CMD to patch file
2020-09-29 18:23:04 +00:00
linux-foldingathome
mafft
mapm3
biology/mapm3: Reformat patches.
2020-09-04 12:24:23 +00:00
migrate
minimap2
molden
mopac
mothur
biology/mothur: fix build on powerpc64le
2020-10-19 10:30:11 +00:00
mrbayes
mummer
biology/mummer: fix build on powerpc64 elfv2 and powerpc64le
2020-10-25 23:03:14 +00:00
muscle
ncbi-blast+
Chase security/p11-kit update
2020-08-30 03:10:23 +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
p5-AcePerl
p5-Bio-ASN1-EntrezGene
p5-Bio-Cluster
p5-Bio-Coordinate
p5-Bio-Das
p5-Bio-Das-Lite
p5-Bio-DB-EMBL
p5-Bio-DB-NCBIHelper
p5-Bio-FeatureIO
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
phrap
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
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: Fix fetch and relax scipy requirement
2020-09-26 09:10:37 +00:00
py-biopython
biology/py-biopython: Upgrade to 1.78
2020-10-16 19:12:43 +00:00
py-bx-python
biology/py-bx-python: Update 0.8.8 -> 0.8.9
2020-06-26 04:17:11 +00:00
py-cutadapt
py-dnaio
py-ete3
Update PyQt to 5.15.0, py-sip to 4.19.24 and qscintilla2 to 2.11.5
2020-10-05 15:50:03 +00:00
py-fastTSNE
py-Genesis-PyAPI
py-gffutils
Unbreak bulk -a
2020-07-14 07:59:28 +00:00
py-gtfparse
biology/py-gtfparse: Update 1.2.0 -> 1.2.1
2020-08-07 04:13:00 +00:00
py-hits
py-loompy
biology/py-loompy: Update 2.0.17 -> 3.0.6
2020-06-16 02:26:08 +00:00
py-macs2
py-multiqc
Unbreak bulk -a
2020-09-19 14:15:42 +00:00
py-orange3-bioinformatics
py-orange3-single-cell
py-pandas-charm
py-pyfaidx
biology/py-pyfaidx: Update 0.5.5.2 -> 0.5.9.1
2020-09-13 19:05:30 +00:00
py-pysam
biology/py-pysam: Update 0.15.4 -> 0.16.0
2020-06-09 05:03:48 +00:00
py-scikit-bio
biology/py-scikit-bio: Fix build on the i386 architecture
2020-09-24 23:16:26 +00:00
py-xenaPython
pyfasta
python-nexus
rainbow
recombine
ruby-bio
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 1.10
2020-08-03 18:22:06 +00:00
scrm
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
stacks
star
stringtie
subread
biology/subread: Add -fcommon for clang 11
2020-09-18 00:57:35 +00:00
tabixpp
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
treekin
treepuzzle
trimadap
trimmomatic
tRNAscan-SE
ugene
vcflib
biology/htslib: Upgrade to 1.10.2
2020-08-03 17:40:04 +00:00
vcftools
velvet
viennarna
biology/viennarna: Update 2.4.14 -> 2.4.15
2020-09-07 21:49:07 +00:00
vsearch
biology/vsearch: Update to 2.15.0
2020-06-20 14:31:59 +00:00
vt
biology/vt: Patch to work with htslib 1.10.2
2020-08-03 17:42:32 +00:00
wise
Makefile
biology/py-biom-format: Restore in preparation for an update to v2.1.8
2020-09-24 19:31:43 +00:00
4c1ed61171