..
angsd
angsd: init at 0.937
2022-03-04 09:17:35 -06:00
ants
treewide: avoid use of lib.optional with list in inputs
2021-10-04 13:02:42 -04:00
aragorn
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
bayescan
bayescan: fix the build
2022-05-13 12:00:08 +02:00
bcftools
bcftools: 1.14 -> 1.15
2022-02-25 11:12:05 -08:00
bedops
bedops: 2.4.39 -> 2.4.40
2021-07-23 01:02:40 +00:00
bedtools
lzma: deprecate alias
2021-04-04 19:49:52 +02:00
bftools
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +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
cmtk: add -std=c++11 to fix build on gcc11
2022-04-15 11:15:30 -05:00
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: 0.8.7 -> 0.9.1
2021-11-25 21:19:48 +11:00
diamond
diamond: switch to fetchFromGitHub
2021-12-23 19:11:17 +01:00
ecopcr
pkgs/applications: rename name to pname&version part 2
2021-11-07 14:53:06 +01:00
eggnog-mapper
eggnog-mapper: 1.0.3 -> 2.1.7
2022-03-18 10:26:47 -05:00
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: mark broken
2022-05-17 10:24:07 -07:00
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
flywheel-cli: init at 16.2.0
2022-03-28 15:54:39 -04:00
freebayes
lzma: deprecate alias
2021-04-04 19:49:52 +02:00
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
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
inormalize
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
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
treewide: move autoconf, automake to nativeBuildInputs
2022-03-30 20:17:24 -05:00
last
last: 1260 -> 1268
2022-03-02 13:35:56 +11:00
MACS2
macs2: init at 2.2.7.1
2021-04-14 10:17:53 -04:00
macse
treewide: convert phases that contain ":" to dont* = true ( #130500 )
2021-07-18 23:42:48 +02:00
manta
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
megahit
Static build for megahit
2022-05-04 02:13:31 +02:00
meme-suite
meme-suite: init at 5.1.1 ( #118603 )
2021-04-05 22:43:27 +02:00
messer-slim
messer-slim: 3.7 -> 3.7.1
2022-02-14 00:46:29 +00:00
migrate
treewide: fix double quoted strings in meta.description
2021-01-24 19:56:59 +07:00
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
mni_autoreg
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
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
mrtrix: 3.0.2 -> unstable-2021-11-25
2021-11-30 21:03:53 -08:00
muscle
treewide: stdenv.lib -> lib
2021-01-16 17:58:11 +07:00
N3
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
neuron
neuron-mpi: remove appendToName to have a consistent package name for repology
2022-02-28 12:46:15 +01:00
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: 0.7.3 -> 0.7.4
2021-05-11 08:46:00 +10:00
paml
treewide: fix double quoted strings in meta.description
2021-01-24 19:56:59 +07:00
picard-tools
treewide: add meta.mainProgram to many packages
2022-04-14 10:24:01 -07:00
platypus
treewide: makeWrapper buildInputs to nativeBuildInputs
2021-02-19 20:09:16 +07:00
plink-ng
treewide: stdenv.lib -> lib
2021-01-16 17:58:11 +07:00
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: remove nativeBuildInputs that are in stdenv
2022-04-16 21:46:46 +03:00
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: 0.8.1 -> 0.8.2 ( #155972 )
2022-01-23 04:51:46 +01:00
samblaster
samblaster: fix darwin build
2021-05-18 13:41:51 +02:00
samtools
Static build for samtools
2022-05-04 02:16:17 +02:00
seaview
seaview: 5.0.4 -> 5.0.5
2021-12-12 15:59:16 +00:00
snpeff
treewide: unzip buildInputs to nativeBuildInputs ( #112302 )
2021-02-20 16:01:53 -05:00
somatic-sniper
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
sortmerna
sortmerna: mark broken on darwin
2021-01-26 12:55:33 -05:00
spades
SPAdes: 3.15.3 -> 3.15.4
2022-02-18 00:55:34 +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
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
subread
subread: init 2.0.3
2021-12-14 13:30:23 +11:00
sumatools
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
svaba
lzma: deprecate alias
2021-04-04 19:49:52 +02:00
tebreak
treewide: remove nativeBuildInputs that are in stdenv
2022-04-16 21:46:46 +03:00
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
varscan: deprecate phases
2021-08-03 00:04:16 +02:00
vcftools
treewide: pkgs.pkgconfig -> pkgs.pkg-config, move pkgconfig to alias.nix
2021-01-19 01:16:25 -08:00
whisper
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
xenomapper
python3Packages.xenomapper: move to top-level
2022-01-01 02:09:11 +01:00
5cf446f41b