nixpkgs/pkgs/applications/science/biology
2023-06-04 19:10:45 +02:00
..
angsd angsd: 0.938 -> 0.940 2022-10-14 14:50:26 +00:00
ants ants: 2.4.3 -> 2.4.4 2023-05-02 12:29:21 -04:00
aragorn
astral treewide: set sourceProvenance for packages containing downloaded jars 2022-06-04 19:47:57 +01:00
bayescan treewide: move NIX_CFLAGS_COMPILE to the env attrset 2023-02-22 21:23:04 +02:00
bcftools bcftools: 1.16 -> 1.17 2023-02-25 23:02:27 +00:00
bedops bedops: fix build on darwin 2023-04-24 22:11:47 +09:00
bedtools bedtools: 2.30.0 -> 2.31.0 2023-04-29 03:05:55 +00:00
bftools treewide: set sourceProvenance for packages containing downloaded jars 2022-06-04 19:47:57 +01:00
blast blast: 2.13.0 -> 2.14.0 2023-05-26 00:23:49 +00:00
bowtie treewide:replace http by https when https is a permanent redirection 2023-02-19 21:47:59 +01:00
bowtie2 bowtie2: 2.4.5 -> 2.5.1 2023-01-21 21:19:00 +00:00
bppsuite
bwa bwa: add runHook 2023-05-15 16:13:49 +09:00
cd-hit
clustal-omega treewide: add meta.mainProgram to many packages 2022-04-14 10:24:01 -07:00
cmtk treewide: move NIX_CFLAGS_COMPILE to the env attrset 2023-02-22 21:23:04 +02:00
conglomerate
dcm2niix treewide: Rename libyamlcpp* to yaml-cpp* 2023-01-31 16:22:54 +01:00
deeptools treewide: switch to nativeCheckInputs 2023-01-21 12:00:00 +00:00
delly delly: 1.1.5 -> 1.1.6 2022-11-08 18:21:37 +00:00
diamond diamond: 2.1.6 -> 2.1.7 2023-06-03 08:46:43 +00:00
dssp dssp: 4.0.5 -> 4.2.2.1 2023-04-14 11:35:48 +09:00
ecopcr ecopcr: 0.8.0 -> 1.0.1 2022-12-08 04:35:53 +01:00
eggnog-mapper eggnog-mapper: 2.1.9 -> 2.1.10 2023-02-11 08:43:59 +00:00
emboss treewide: replace http by https when https is a permanent redirection 2023-01-22 02:46:49 +01:00
est-sfs
exonerate
EZminc EZminc: itk4 -> itk (formally; package is broken) 2022-09-04 13:36:24 -04:00
fastp fastp: 0.23.3 -> 0.23.4 2023-06-04 03:21:21 +00:00
febio-studio treewide: make ffmpeg_4-dependant packages depend on ffmpeg_4 2023-03-13 16:42:22 -06:00
flywheel-cli treewide/applications: add sourceType binaryNativeCode for many packages 2022-06-23 18:38:19 +01:00
freebayes treewide: move NIX_CFLAGS_COMPILE to the env attrset 2023-02-22 21:23:04 +02:00
gatk gatk: 4.3.0.0 -> 4.4.0.0 2023-03-18 01:10:14 +00:00
genmap treewide: switch to nativeCheckInputs 2023-01-21 12:00:00 +00:00
hh-suite hh-suite: init at 3.3.0 2023-04-19 10:32:35 +09:00
hisat2
hmmer
igv igv: 2.16.0 -> 2.16.1 2023-05-31 13:33:15 +00:00
inormalize inormalize/minc-widgets/gimp-plugins: use pname & version 2023-02-12 22:21:44 +01:00
iqtree iqtree: 2.2.2.4 -> 2.2.2.6 2023-05-30 01:13:17 +00:00
itsx
iv
jbrowse jbrowse: init at 2.5.0 2023-05-12 11:24:26 -07:00
kallisto
kent kent: package headers too. 2023-05-06 19:48:14 +02:00
kssd kssd: pull upstream fix for -fno-common tollchains 2022-05-21 11:22:53 +01:00
last last: 1447 -> 1453 2023-04-03 08:38:27 +10:00
MACS2 treewide/applications: use top-level fetchPypi 2023-05-25 10:51:30 -04:00
macse treewide: set sourceProvenance for packages containing downloaded jars 2022-06-04 19:47:57 +01:00
mafft mafft: 7.515 -> 7.520 2023-04-12 13:28:24 +09:00
manta
megahit treewide: optional -> optionals where the argument is a list 2022-10-10 15:40:21 +03:00
meme-suite pkgs.applications: remove unused args 2022-10-12 16:00:16 +02:00
messer-slim messer-slim: 4.0 -> 4.0.1 2022-09-15 22:25:51 +00:00
migrate treewide: pkgs/applications: mark broken for darwin 2022-05-29 10:56:04 +02:00
minc-tools
minc-widgets inormalize/minc-widgets/gimp-plugins: use pname & version 2023-02-12 22:21:44 +01:00
minia treewide: move NIX_CFLAGS_COMPILE to the env attrset 2023-02-22 21:23:04 +02:00
minimap2 minimap2: 2.25 -> 2.26 2023-05-03 19:38:48 +00:00
mmseqs2 mmseqs2: init at 14-7e284 2022-10-31 23:49:10 +09:00
mni_autoreg mni_autoreg: unstable-2017-02-22 -> unstable-2022-05-20 2022-07-26 16:03:12 -04:00
mosdepth
mrbayes
mrtrix treewide: switch to nativeCheckInputs 2023-01-21 12:00:00 +00:00
muscle muscle: fix pname 2023-01-28 04:20:00 +00:00
N3
nest nest: specify license 2023-03-18 11:23:52 +01:00
neuron treewide: fix lints 2023-03-11 00:55:17 +02:00
niftyreg treewide: move NIX_CFLAGS_COMPILE to the env attrset 2023-02-22 21:23:04 +02:00
niftyseg
obitools
octopus treewide: move NIX_CFLAGS_COMPILE to the env attrset 2023-02-22 21:23:04 +02:00
paml treewide: move NIX_CFLAGS_COMPILE to the env attrset 2023-02-22 21:23:04 +02:00
picard-tools picard-tools: 2.27.5 -> 3.0.0 2023-03-01 14:43:38 +00:00
platypus
plink-ng treewide: use optionalString 2023-02-13 21:52:34 +01:00
poretools
prodigal
quast treewide: python{ => .pythonForBuild}.interpreter 2023-02-26 20:26:17 +00:00
raxml raxml-mpi: remove appendToName to have a consistent package name for repology 2022-02-28 12:46:15 +01:00
repseek
sambamba sambamba: 0.8.2 -> 1.0.0 2023-01-22 13:54:41 +00:00
samblaster
samtools Samtools: 1.13 -> 1.17 2023-04-12 12:00:25 +02:00
seaview treewide:replace http by https when https is a permanent redirection 2023-02-19 21:47:59 +01:00
seqkit seqkit: 2.3.1 -> 2.4.0 2023-03-21 10:45:22 +00:00
seqtk seqtk: 1.3 -> 1.4 2023-05-28 06:48:51 +00:00
snpeff treewide: replace http by https when https is a permanent redirection 2023-01-22 02:46:49 +01:00
somatic-sniper
sortmerna pkgs.applications: remove unused args 2022-10-12 16:00:16 +02:00
spades Merge pull request #184694 from r-ryantm/auto-update/SPAdes 2022-08-23 20:21:42 +02:00
sratoolkit sratoolkit: init at 2.11.3 2022-11-21 20:27:28 +01:00
stacks stacks: 2.60 -> 2.62 2023-02-06 21:36:49 +01:00
star star: 2.7.10a -> 2.7.10b 2023-01-14 06:06:52 +00:00
strelka treewide: move NIX_CFLAGS_COMPILE to the env attrset 2023-02-22 21:23:04 +02:00
subread subread: 2.0.5 -> 2.0.6 2023-05-10 22:30:35 +10:00
sumatools
svaba treewide: move NIX_CFLAGS_COMPILE to the env attrset 2023-02-22 21:23:04 +02:00
tandem-aligner tandem-aligner: add changelog to meta 2023-04-19 21:23:21 +09:00
tebreak treewide: remove nativeBuildInputs that are in stdenv 2022-04-16 21:46:46 +03:00
treemix treemix: init at 1.13 2022-09-05 06:55:03 +02:00
trf trf: init at 4.09.1 2023-03-19 22:25:42 +09:00
trimal
truvari truvari: add patches to fix truvari anno 2023-05-15 10:01:38 +09:00
varscan varscan: 2.4.5 -> 2.4.6 2023-04-05 14:55:31 +00:00
vcftools treewide: move pkg-config, autoreconfHook, intltool to nativeBuildInputs 2022-09-26 17:53:26 +03:00
veryfasttree veryfasttree: fix pname 2023-01-28 04:20:00 +00:00
whisper treewide: pkgs/applications: mark broken for darwin 2022-05-29 10:56:04 +02:00
xenomapper