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2bfa93e01c
nixpkgs/pkgs/applications/science/biology
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Alyssa Ross 2bfa93e01c
treewide: python{ => .pythonForBuild}.interpreter 
It won't be enough to fix cross in all cases, but it is in at least
one: pywayland.  I've only made the change in cases I'm confident it's
correct, as it would be wrong to change this when python.interpreter
is used in wrappers, and possibly when it's used for running tests.
2023-02-26 20:26:17 +00:00
..
angsd angsd: 0.938 -> 0.940 2022-10-14 14:50:26 +00:00
ants ants: unpin vtk dependency 2023-01-27 00:21:26 -05:00
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: 1.15 -> 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 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 treewide: replace http by https when https is a permanent redirection 2023-01-22 02:46:49 +01:00
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: 2.1.0 -> 2.1.1 2023-02-10 02:56:54 +00:00
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: 2.1.9 -> 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
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 treewide: move NIX_CFLAGS_COMPILE to the env attrset 2023-02-22 21:23:04 +02:00
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
igv igv: 2.15.5 -> 2.16.0 2023-02-04 18:01:58 +00:00
inormalize inormalize/minc-widgets/gimp-plugins: use pname & version 2023-02-12 22:21:44 +01:00
iqtree iqtree: init at 2.2.0.4 2022-05-30 10:53:40 +02:00
itsx
iv
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: 1445 -> 1447 2023-02-12 17:14:30 +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 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: 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
nest nest: fix Python & Darwin 2023-02-25 10:28:59 -05:00
neuron neuron: 7.5 -> 8.2.1 2023-02-21 13:52:34 -05:00
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: 2.27.4 -> 2.27.5 2022-10-08 00:09:59 +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 Merge pull request #212002 from mothsART/feature/replace_http_by_https 2023-01-22 03:26:02 +01:00
seaview treewide:replace http by https when https is a permanent redirection 2023-02-19 21:47:59 +01:00
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: 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 treewide: replace http by https when https is a permanent redirection 2023-01-22 02:46:49 +01:00
sumatools
svaba treewide: move NIX_CFLAGS_COMPILE to the env attrset 2023-02-22 21:23:04 +02:00
tandem-aligner tandem-aligner: fix build with GCC 12 2023-02-25 13:40:11 +01:00
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 varscan: 2.4.4 -> 2.4.5 2023-02-05 13:38:28 +00:00
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