| .. |
|
abyss
|
|
|
|
artemis
|
|
|
|
avida
|
|
|
|
babel
|
|
|
|
bamtools
|
|
|
|
bcftools
|
biology/bcftools: Upgrade to 1.10.2
|
2020-08-03 18:16:54 +00:00 |
|
bedtools
|
|
|
|
bioawk
|
|
|
|
biococoa
|
|
|
|
bolt-lmm
|
|
|
|
bowtie
|
|
|
|
bowtie2
|
|
|
|
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: Upgrade to 2020.09.12
|
2020-09-22 00:55:39 +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 2.5.18 and add AVX option
|
2020-09-02 17:47:10 +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
|
|
|
|
linux-foldingathome
|
|
|
|
mafft
|
|
|
|
mapm3
|
biology/mapm3: Reformat patches.
|
2020-09-04 12:24:23 +00:00 |
|
migrate
|
|
|
|
minimap2
|
|
|
|
molden
|
|
|
|
mopac
|
|
|
|
mothur
|
|
|
|
mrbayes
|
|
|
|
mummer
|
|
|
|
muscle
|
|
|
|
ncbi-blast+
|
Chase security/p11-kit update
|
2020-08-30 03:10:23 +00:00 |
|
ncbi-cxx-toolkit
|
biology/ncbi-cxx-toolkit: Update 21.0.0 -> 22.0.0
|
2020-09-25 06:57:43 +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
|
|
|
|
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
|
|
|
|
primer3
|
|
|
|
prodigal
|
|
|
|
prodigy-lig
|
|
|
|
protomol
|
|
|
|
psi88
|
|
|
|
py-biom-format
|
biology/py-biom-format: Update to version 2.1.8
|
2020-09-25 01:03:03 +00:00 |
|
py-biopython
|
|
|
|
py-bx-python
|
|
|
|
py-cutadapt
|
|
|
|
py-dnaio
|
|
|
|
py-ete3
|
biology/py-ete3: Update 3.1.1 -> 3.1.2
|
2020-09-02 03:54:04 +00:00 |
|
py-fastTSNE
|
|
|
|
py-Genesis-PyAPI
|
|
|
|
py-gffutils
|
|
|
|
py-gtfparse
|
biology/py-gtfparse: Update 1.2.0 -> 1.2.1
|
2020-08-07 04:13:00 +00:00 |
|
py-hits
|
|
|
|
py-loompy
|
|
|
|
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
|
|
|
|
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
|
|
|
|
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
|
|
|
|
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 |
