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nixpkgs/pkgs/applications/science/biology
History
Guillaume Girol 33afbf39f6 treewide: switch to nativeCheckInputs 
checkInputs used to be added to nativeBuildInputs. Now we have
nativeCheckInputs to do that instead. Doing this treewide change allows
to keep hashes identical to before the introduction of
nativeCheckInputs.
2023-01-21 12:00:00 +00:00
..
angsd angsd: 0.938 -> 0.940 2022-10-14 14:50:26 +00:00
ants ants: 2.4.2 -> 2.4.3 2023-01-09 09:48:53 -06:00
aragorn
astral treewide: set sourceProvenance for packages containing downloaded jars 2022-06-04 19:47:57 +01:00
bayescan bayescan: fix the build 2022-05-13 12:00:08 +02:00
bcftools bcftools: 1.15 -> 1.16 2022-08-18 18:44:42 +00:00
bedops bedops: 2.4.40 -> 2.4.41 2022-07-19 09:09:52 +10:00
bedtools
bftools treewide: set sourceProvenance for packages containing downloaded jars 2022-06-04 19:47:57 +01:00
blast blast: 2.12.0 -> 2.13.0 2022-04-29 09:39:10 -05:00
bowtie bowtie: fix build on case insensitive file systems 2022-05-11 03:20:03 -05:00
bowtie2 bowtie2: 2.4.4 -> 2.4.5 2022-01-23 22:45:59 +00:00
bppsuite
bwa bwa: pull upstream fix for -fno-common tollchains 2022-05-08 08:56:43 +01:00
cd-hit
clustal-omega treewide: add meta.mainProgram to many packages 2022-04-14 10:24:01 -07:00
cmtk treewide: pkgs/applications: mark broken for darwin 2022-05-29 10:56:04 +02:00
conglomerate
dcm2niix dcm2niix: support usage of suggested Cloudflare zlib 2022-04-18 15:00:45 -04:00
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: update metadata 2022-07-13 12:33:33 +02:00
dssp dssp: init at 4.0.5 2022-07-19 12:17:34 +09:00
ecopcr ecopcr: 0.8.0 -> 1.0.1 2022-12-08 04:35:53 +01:00
eggnog-mapper eggnog-mapper: 2.1.7 -> 2.1.9 2022-08-21 12:45:21 +00:00
emboss pkgs/applications: rename name to pname&version part 2 2021-11-07 14:53:06 +01:00
est-sfs
exonerate
EZminc EZminc: itk4 -> itk (formally; package is broken) 2022-09-04 13:36:24 -04:00
fastp fastp: 0.23.1 -> 0.23.2 2021-12-02 08:03:17 +11:00
febio-studio febio-studio: init at 1.6.1 2022-02-21 16:43:36 +01:00
flywheel-cli treewide/applications: add sourceType binaryNativeCode for many packages 2022-06-23 18:38:19 +01:00
freebayes freebayes: add -fcommon workaround 2022-05-14 13:19:17 +01:00
gatk gatk: 4.2.6.1 -> 4.3.0.0 2022-10-16 21:48:30 +08:00
genmap treewide: switch to nativeCheckInputs 2023-01-21 12:00:00 +00:00
hisat2 hisat2: update homepage 2022-02-06 15:10:53 +01:00
hmmer hmmer: restrict platforms to x86_64 2021-11-20 19:17:57 +00:00
igv igv: 2.15.1 -> 2.15.4 2023-01-03 14:36:54 +08:00
inormalize
iqtree iqtree: init at 2.2.0.4 2022-05-30 10:53:40 +02:00
itsx
iv pkgs/applications: rename name to pname&version part 2 2021-11-07 14:53:06 +01:00
kallisto kallisto: 0.46.2 -> 0.48.0 2022-01-31 09:53:54 -08:00
kent
kssd kssd: pull upstream fix for -fno-common tollchains 2022-05-21 11:22:53 +01:00
last last: 1409 -> 1411 2022-09-21 08:24:01 +00:00
MACS2 MACS2: mark broken 2022-06-06 11:46:22 -07:00
macse treewide: set sourceProvenance for packages containing downloaded jars 2022-06-04 19:47:57 +01:00
mafft mafft: 7.505 -> 7.508 2022-09-09 13:26:38 +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
minia
minimap2 minimap2: enable aarch64 builds (#161169) 2022-03-04 12:27:29 +01:00
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 mosdepth: 0.3.2 -> 0.3.3 2022-02-12 14:31:47 +00:00
mrbayes
mrtrix treewide: switch to nativeCheckInputs 2023-01-21 12:00:00 +00:00
muscle muscle: add myself to maintainers 2022-11-22 20:19:17 +01:00
N3
neuron treewide: optional -> optionals where the argument is a list 2022-10-10 15:40:21 +03:00
niftyreg
niftyseg niftyseg: switch to fetchFromGitHub 2021-12-23 19:11:17 +01:00
obitools obitools3: removed useless python restriction 2021-11-08 07:51:48 +01:00
octopus octopus-caller: backport patch to fix build 2022-10-25 09:52:28 +11:00
paml paml: add -fcommon workaround 2022-05-22 20:23:12 +01:00
picard-tools picard-tools: 2.26.11 -> 2.27.4 2022-07-29 16:12:10 +00:00
platypus
plink-ng treewide: pkgs/applications: mark broken for aarch64-linux 2022-05-30 13:42:58 +02:00
poretools python,pythonPackages: make aliases 2022-01-16 18:39:59 +00:00
prodigal
quast treewide/applications: add sourceType binaryNativeCode for many packages 2022-06-23 18:38:19 +01:00
raxml raxml-mpi: remove appendToName to have a consistent package name for repology 2022-02-28 12:46:15 +01:00
repseek repseek: init at 9Sep2014 (#148017) 2022-01-31 14:59:32 +01:00
sambamba sambamba: fix compilation on Darwin, cleanup installPhase 2022-10-23 16:12:47 +02:00
samblaster
samtools treewide: switch to nativeCheckInputs 2023-01-21 12:00:00 +00:00
seaview seaview: 5.0.4 -> 5.0.5 2021-12-12 15:59:16 +00:00
seqkit seqkit: init at 2.3.1 2022-11-04 08:51:32 +01:00
seqtk seqtk: init at 1.3 2022-09-25 19:55:58 -04:00
snpeff treewide: set sourceProvenance for packages containing downloaded jars 2022-06-04 19:47:57 +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: 2.59 -> 2.60 2022-01-02 19:23:58 +01:00
star star: 2.7.9a -> 2.7.10a 2022-01-24 19:51:44 +01:00
strelka
subread treewide: pkgs/applications: mark broken for darwin 2022-05-29 10:56:04 +02:00
sumatools
svaba Merge pull request #175259 from trofi/workaround-fno-common-for-svaba 2022-06-03 05:59:16 +00:00
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
trimal
truvari python310Packages.levenshtein: don't use alias 2023-01-09 06:09:31 -08:00
varscan treewide: set sourceProvenance for packages containing downloaded jars 2022-06-04 19:47:57 +01:00
vcftools treewide: move pkg-config, autoreconfHook, intltool to nativeBuildInputs 2022-09-26 17:53:26 +03:00
veryfasttree veryfasttree: init at 3.1.1 2022-11-22 20:45:45 +01:00
whisper treewide: pkgs/applications: mark broken for darwin 2022-05-29 10:56:04 +02:00
xenomapper python3Packages.xenomapper: move to top-level 2022-01-01 02:09:11 +01:00