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nixpkgs/pkgs/applications/science/biology
History
Sergei Trofimovich 8147fb683c samtools: pull upstream fix for ncurses-6.3 
Without the fix build on ncurses-6.3 fails as:

    bam_tview_curses.c:88:5: error: format not a string literal and no format arguments [-Werror=format-security]
       88 |     mvprintw(y,x,str);
          |     ^~~~~~~~
2021-11-26 13:02:05 +00:00
..
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 treewide: stdenv.lib -> lib 2021-01-16 17:58:11 +07:00
bcftools bcftools: 1.13 -> 1.14 2021-10-29 02:49:14 +00:00
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: 2.11.0 -> 2.12.0 2021-09-15 15:33:44 +00:00
bowtie bowtie: 1.3.0 -> 1.3.1 2021-09-15 07:35:44 +00:00
bowtie2 Merge pull request #111691 from jbedo/bowtie2 2021-08-07 04:03:47 +03:00
bppsuite
bwa treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
cd-hit perlPackages.ImageMagick: rename from perlPackages.PerlMagick 2021-08-02 20:05:00 +03:00
clustal-omega treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
cmtk pkgs/applications: rename name to pname&version part 2 2021-11-07 14:53:06 +01:00
conglomerate treewide: stdenv.lib -> lib 2021-01-16 17:58:11 +07:00
dcm2niix dcm2niix: 1.0.20210317 -> 1.0.20211006 2021-10-29 09:34:20 +00:00
deeptools deeptools: Fix tests 2020-11-25 21:36:37 +01:00
delly delly: 0.8.7 -> 0.9.1 2021-11-25 21:19:48 +11:00
diamond pkgs/applications: rename name to pname&version part 2 2021-11-07 14:53:06 +01:00
ecopcr pkgs/applications: rename name to pname&version part 2 2021-11-07 14:53:06 +01:00
eggnog-mapper treewide: makeWrapper buildInputs to nativeBuildInputs 2021-02-19 20:09:16 +07:00
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 treewide: pkgs.pkgconfig -> pkgs.pkg-config, move pkgconfig to alias.nix 2021-01-19 01:16:25 -08:00
fastp fastp: 0.22.0 -> 0.23.1 2021-10-19 21:09:05 +11:00
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 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 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: 1179 -> 1256 2021-10-19 13:23:14 +11:00
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: 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 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 minimap2: 2.17 -> 2.22 2021-08-14 15:55:35 +00:00
mni_autoreg treewide: with stdenv.lib; in meta -> with lib; 2021-01-11 10:38:22 +01:00
mosdepth mosdepth: convert to buildNimPackage 2021-09-05 11:20:02 +02:00
mrbayes mrbayes: 3.2.7 -> 3.2.7a 2021-07-27 14:30:23 +02:00
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 treewide: ensure pre/post phase hooks are strings 2021-08-20 19:08:42 -04:00
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 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 picard-tools: 2.26.3 -> 2.26.4 2021-11-03 19:57:00 +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 0.8.0 -> 0.8.1 2021-08-31 12:37:49 +03:00
samblaster samblaster: fix darwin build 2021-05-18 13:41:51 +02:00
samtools samtools: pull upstream fix for ncurses-6.3 2021-11-26 13:02:05 +00:00
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: 3.15.2 -> 3.15.3 2021-08-15 11:12:42 +03:00
stacks Merge pull request #135516 from bzizou/stacks 2021-08-26 03:50:48 +02:00
star star: 2.7.8a -> 2.7.9a 2021-09-24 10:37:28 +08:00
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: 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