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nixpkgs/pkgs/applications/science/biology
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Stéphan Kochen c47425a230 sambamba: fix darwin build
2021-05-22 20:56:09 +02:00
..
ants
treewide: stdenv.lib -> lib
2021-01-16 17:58:11 +07:00
aragorn
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
bayescan
treewide: stdenv.lib -> lib
2021-01-16 17:58:11 +07:00
bcftools
lzma: deprecate alias
2021-04-04 19:49:52 +02:00
bedops
bedops: init 2.4.39
2021-03-28 22:27:51 -04:00
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: 2.10.0 -> 2.11.0
2021-02-06 19:20:56 +00:00
bowtie
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
bowtie2
bowtie2: 2.4.2 -> 2.4.3
2021-05-16 02:53:03 -04:00
bppsuite
…
bwa
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
cd-hit
cd-hit: fix darwin build (#123026)
2021-05-14 17:27:16 -04:00
clustal-omega
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
cmtk
treewide: stdenv.lib -> lib
2021-01-16 17:58:11 +07:00
conglomerate
treewide: stdenv.lib -> lib
2021-01-16 17:58:11 +07:00
dcm2niix
dcm2niix: 1.0.20201102 -> 1.0.20210317
2021-05-02 11:10:40 +00:00
deeptools
deeptools: Fix tests
2020-11-25 21:36:37 +01:00
delly
lzma: deprecate alias
2021-04-04 19:49:52 +02:00
diamond
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
ecopcr
ecopcr: use spaces for indentation
2021-01-20 10:53:10 +10:00
eggnog-mapper
treewide: makeWrapper buildInputs to nativeBuildInputs
2021-02-19 20:09:16 +07:00
emboss
treewide: stdenv.lib -> lib
2021-01-16 17:58:11 +07:00
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
treewide: pkgs.pkgconfig -> pkgs.pkg-config, move pkgconfig to alias.nix
2021-01-19 01:16:25 -08:00
fastp
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
freebayes
lzma: deprecate alias
2021-04-04 19:49:52 +02:00
hisat2
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
hmmer
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
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
treewide: stdenv.lib -> lib
2021-01-16 17:58:11 +07:00
kallisto
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
kent
lzma: deprecate alias
2021-04-04 19:49:52 +02:00
kssd
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
last
last: 1178 -> 1179
2021-02-21 21:24:17 +00:00
lumpy
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
MACS2
macs2: init at 2.2.7.1
2021-04-14 10:17:53 -04:00
macse
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
manta
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
megahit
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
meme-suite
meme-suite: init at 5.1.1 (#118603)
2021-04-05 22:43:27 +02:00
messer-slim
messer-slim: 3.2.1 -> 3.6
2021-03-04 18:40:37 +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
treewide: editorconfig fixes
2021-01-20 09:11:11 +10:00
mni_autoreg
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
mosdepth
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
mrbayes
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
mrtrix
mrtrix: 3.0.0 -> 3.0.2
2020-09-30 22:13:18 -04:00
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
ncbi-tools
treewide: fix double quoted strings in meta.description
2021-01-24 19:56:59 +07:00
neuron
mpi: use mpi attribute consistently as the default MPI implementations
2021-01-23 12:15:13 +01:00
niftyreg
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
niftyseg
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
obitools
treewide: remove stdenv where not needed
2021-01-25 18:31:47 +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
picard-tools: 2.25.0 -> 2.25.1
2021-03-26 03:16:44 +00:00
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
treewide: remove stdenv where not needed
2021-01-25 18:31:47 +01:00
prodigal
treewide: add targetPrefix to hardcoded references to CC=cc
2021-02-20 01:01:46 +07:00
quast
treewide: stdenv.lib -> lib
2021-01-16 17:58:11 +07:00
raxml
mpi: use mpi attribute consistently as the default MPI implementations
2021-01-23 12:15:13 +01:00
sambamba
sambamba: fix darwin build
2021-05-22 20:56:09 +02:00
samblaster
samblaster: fix darwin build
2021-05-18 13:41:51 +02:00
samtools
treewide: stdenv.lib -> lib
2021-01-16 17:58:11 +07:00
seaview
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
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: 3.15.1 -> 3.15.2 + fix license and platform
2021-03-23 10:51:01 +01:00
stacks
stacks: 2.53 -> 2.55
2021-03-09 17:19:55 +00:00
star
star: 2.7.7a -> 2.7.8a
2021-02-23 10:38:00 +00:00
strelka
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
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 stdenv where not needed
2021-01-25 18:31:47 +01:00
trimal
treewide: with stdenv.lib; in meta -> with lib;
2021-01-11 10:38:22 +01:00
truvari
truvari: 1.3.4 -> 2.0.2, fixing build
2020-09-20 12:25:17 +01:00
varscan
treewide: makeWrapper buildInputs to nativeBuildInputs
2021-02-19 20:09:16 +07:00
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
…