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9bd2506458
nixpkgs/pkgs/applications/science/biology
History
Atemu 9bd2506458 treewide: make ffmpeg_4-dependant packages depend on ffmpeg_4 
These packages were identified as broken when ffmpeg = ffmpeg_5.

Tested _only_ by building them. If you are a maintainer of one of these
packages, please test whether your package still works.
2023-03-13 16:42:22 -06:00
..
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: 1.16 -> 1.17 2023-02-25 23:02:27 +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: 2.1.4 -> 2.1.5 2023-03-11 18:22:58 +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 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: 4.2.6.1 -> 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-full: 8.2.1 -> 8.2.2 2023-02-26 05:18:37 +00:00
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 python,pythonPackages: make aliases 2022-01-16 18:39:59 +00:00
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 repseek: init at 9Sep2014 (#148017) 2022-01-31 14:59:32 +01:00
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