..
angsd
angsd: pull patch pending upstream inclusion for parallel build fix
2023-08-20 08:50:53 +01:00
ants
ants: 2.5.0 -> 2.5.1
2024-01-26 01:12:12 +01:00
aragorn
aragorn: fix format
2023-06-08 18:42:29 +09:00
astral
bamtools
bamtools: init at 2.5.2
2023-08-18 00:17:15 +09:00
bayescan
bcftools
bcftools: 1.18 -> 1.19
2023-12-13 06:48:21 +00:00
bedops
bedops: fix build on darwin
2023-04-24 22:11:47 +09:00
bedtools
bedtools: 2.31.0 -> 2.31.1
2023-11-09 06:18:08 +00:00
bftools
bioawk
bioawk: init at unstable-2017-09-11
2023-08-18 00:36:09 +09:00
blast
blast-bin: add sourceProvenance to meta
2023-10-07 10:12:24 +09:00
bowtie
bowtie2
bowtie2: 2.5.2 -> 2.5.3
2024-01-18 01:41:31 +00:00
bppsuite
bppsuite: fix homepage
2023-06-15 12:18:11 -04:00
bwa
bwa: add runHook
2023-05-15 16:13:49 +09:00
bwa-mem2
bwa-mem2: init at version 2.2.1
2023-08-23 15:02:06 -07:00
cd-hit
clustal-omega
cmtk
cmtk: fix format
2023-07-11 17:50:47 +09:00
conglomerate
dcm2niix
deeptools
deeptools: fix build
2024-01-28 12:17:37 -08:00
delly
delly: 1.1.8 -> 1.2.6
2023-12-22 18:36:25 +00:00
diamond
diamond: 2.1.7 -> 2.1.8
2023-06-25 04:35:30 +00:00
dssp
dssp: 4.4.4.1 -> 4.4.5
2023-11-24 22:34:06 +09:00
ecopcr
eggnog-mapper
eggnog-mapper: 2.1.10 -> 2.1.12
2024-01-18 19:17:47 +00:00
emboss
est-sfs
exonerate
EZminc
fastp
fastp: 0.23.3 -> 0.23.4
2023-06-04 03:21:21 +00:00
febio-studio
flywheel-cli
treewide: s_targetPlatform_hostPlatform_ in non-compiler packages
2023-11-17 08:07:34 +00:00
freebayes
gatk
gatk: 4.4.0.0 -> 4.5.0.0
2023-12-15 04:20:42 +00:00
genmap
hh-suite
hh-suite: fix build on GCC 13
2024-02-08 21:54:47 +00:00
hisat2
hmmer
hmmer: add changelog to meta
2023-09-24 04:24:00 +00:00
igv
igv: use jdk17 instead of jdk11 ( #285521 )
2024-02-01 14:42:34 +01:00
inormalize
inormalize: fix build on darwin
2024-01-21 23:26:55 +01:00
iqtree
iqtree: 2.2.2.6 -> 2.2.2.7
2023-08-25 12:25:13 +00:00
itsx
iv
jbrowse
jbrowse: init at 2.5.0
2023-05-12 11:24:26 -07:00
kalign
kalign: 3.3.5 -> 3.4.0
2023-12-11 06:26:11 +00:00
kallisto
kallisto: 0.50.0 -> 0.50.1
2023-11-02 11:02:00 +00:00
kent
perlPackages.BioBigFile: Addressing reviewer change
2023-11-21 23:16:39 +01:00
kssd
kssd: enable aarch64-linux support & tests
2023-11-03 19:34:28 +09:00
last
last: 1519 -> 1540
2024-02-06 06:07:25 +00:00
macs2
macs2: 2.2.8 -> 2.2.9.1
2023-08-11 14:45:45 -07:00
macse
mafft
manta
megahit
meme-suite
messer-slim
messer-slim: 4.0.1 -> 4.1
2023-12-16 20:13:33 +00:00
migrate
minc-tools
minc-widgets
minia
minimap2
minimap2: 2.25 -> 2.26
2023-05-03 19:38:48 +00:00
mmseqs2
mmseqs2: 14-7e284 -> 15-6f452
2023-11-01 09:19:34 +00:00
mni_autoreg
mrbayes
mrtrix
mrtrix: unstable-2021-11-25 -> 3.0.4
2023-09-06 12:11:38 -04:00
muscle
treewide: noop: refer to src.name or similar in sourceRoot where appropriate, part 1: trivial cases
2023-08-03 16:32:03 +00:00
N3
n3: fix build on darwin
2024-01-21 23:22:54 +01:00
nest
nest-mpi: 3.5 -> 3.6
2023-09-30 18:54:13 +00:00
neuron
neuron-mpi: 8.2.2 -> 8.2.3
2023-09-23 02:33:53 +00:00
niftyreg
niftyseg
obitools
treewide: replace lib/${python.libPrefix}/site-packages with its shorthand ${python.sitePackages}
2024-01-30 19:56:57 +01:00
octopus
various packages: pin boost179
2023-07-22 16:54:22 +02:00
paml
paml: refactor
2023-07-14 15:08:14 +09:00
picard-tools
picard-tools: 3.1.0 -> 3.1.1
2023-11-15 14:35:32 +00:00
platypus
plink-ng
poretools
poretools: mark as broken
2023-12-11 04:28:39 +00:00
prodigal
quast
treewide: change pythonForBuild to pythonOnBuildForHost
2023-11-05 17:42:12 -08:00
raxml
raxml: 8.2.12 -> 8.2.13
2023-10-16 22:16:12 +00:00
repseek
sambamba
sambamba: 1.0.0 -> 1.0.1
2023-08-25 06:20:00 +00:00
samblaster
samtools
samtools: 1.19 -> 1.19.2
2024-01-28 12:24:10 -08:00
seaview
seqkit
seqkit: 2.6.1 -> 2.7.0
2024-02-01 04:24:02 +00:00
seqtk
seqtk: 1.3 -> 1.4
2023-05-28 06:48:51 +00:00
snpeff
somatic-sniper
sortmerna
treewide: replace -DCMAKE_BUILD_TYPE in cmakeFlags with cmakeBuildType
2023-09-08 14:18:26 +00:00
spades
SPAdes: fix build
2024-01-20 15:28:48 -03:00
sratoolkit
treewide: remove unneeded dots and slashes in sourceRoots
2023-08-12 08:29:56 +00:00
stacks
stacks: 2.65 -> 2.66
2024-01-24 07:54:36 +00:00
star
treewide: noop: refer to src.name or similar in sourceRoot where appropriate, part 1: trivial cases
2023-08-03 16:32:03 +00:00
strelka
strelka: add aarch64-linux support
2023-12-11 13:37:17 +01:00
subread
subread: 2.0.5 -> 2.0.6
2023-05-10 22:30:35 +10:00
sumatools
svaba
svaba: fix gcc-13 build failure
2024-02-11 09:59:19 +00:00
tandem-aligner
treewide: noop: refer to src.name or similar in sourceRoot where appropriate, part 1: trivial cases
2023-08-03 16:32:03 +00:00
tebreak
treemix
trf
trimal
treewide: remove execute bit for non-executable *.nix files
2023-10-20 19:55:39 +02:00
trimmomatic
trimmomatic: make deterministic and clean up
2024-01-04 21:45:11 +01:00
truvari
truvari: 4.0.0 -> 4.1.0
2023-10-07 01:30:27 +09:00
varscan
vcftools
treewide: remove execute bit for non-executable *.nix files
2023-10-20 19:55:39 +02:00
veryfasttree
veryfasttree: 4.0.2 -> 4.0.3
2023-09-12 06:13:28 +00:00
whisper
whisper: enable parallel building
2024-01-25 19:27:12 +00:00
xenomapper
a59d5e3028