nixpkgs/pkgs/applications/science/biology
2022-11-08 18:21:37 +00:00
..
angsd angsd: 0.938 -> 0.940 2022-10-14 14:50:26 +00:00
ants ants: 2.4.1 -> 2.4.2 2022-10-19 09:19:31 +08:00
aragorn treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
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 lzma: deprecate alias 2021-04-04 19:49:52 +02:00
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 perlPackages.ImageMagick: rename from perlPackages.PerlMagick 2021-08-02 20:05:00 +03:00
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 treewide: stdenv.lib -> lib 2021-01-16 17:58:11 +07:00
dcm2niix dcm2niix: support usage of suggested Cloudflare zlib 2022-04-18 15:00:45 -04:00
deeptools deeptools: 3.5.0 -> 3.5.1 2022-01-21 05:36:24 +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 maintainers: remove metabar 2022-06-29 00:52:13 +02:00
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 est-sfs: fix darwin build 2021-05-15 12:10:05 +02:00
exonerate treewide: pkgs.pkgconfig -> pkgs.pkg-config, move pkgconfig to alias.nix 2021-01-19 01:16:25 -08:00
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 genmap: init 1.3.0 2021-12-04 06:51:16 +11:00
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: 2.14.0 -> 2.14.1 2022-09-05 22:29:15 +00:00
inormalize treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
iqtree iqtree: init at 2.2.0.4 2022-05-30 10:53:40 +02:00
itsx treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
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 lzma: deprecate alias 2021-04-04 19:49:52 +02:00
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 treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
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 treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
minc-widgets treewide: stdenv.lib -> lib 2021-01-16 17:58:11 +07:00
minia treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
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 mrbayes: 3.2.7 -> 3.2.7a 2021-07-27 14:30:23 +02:00
mrtrix treewide: pkgs/applications: mark broken for aarch64-linux 2022-05-30 13:42:58 +02:00
muscle treewide: pkgs/applications: mark broken for aarch64-linux 2022-05-30 13:42:58 +02:00
N3 treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
neuron treewide: optional -> optionals where the argument is a list 2022-10-10 15:40:21 +03:00
niftyreg treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
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 treewide: makeWrapper buildInputs to nativeBuildInputs 2021-02-19 20:09:16 +07:00
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 treewide: add targetPrefix to hardcoded references to CC=cc 2021-02-20 01:01:46 +07:00
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 samblaster: fix darwin build 2021-05-18 13:41:51 +02:00
samtools treewide: optional -> optionals where the argument is a list 2022-10-10 15:40:21 +03:00
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 treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
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
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 treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
subread treewide: pkgs/applications: mark broken for darwin 2022-05-29 10:56:04 +02:00
sumatools treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
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 treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
truvari truvari: 2.0.2 -> 2.1.1 (#126839) 2021-06-15 22:14:20 +02:00
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
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