Martin Weinelt 8a085cd8e3 Merge remote-tracking branch 'origin/master' into staging-next		2023-03-05 15:36:16 +01:00
..
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
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
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: 2.1.3 -> 2.1.4	2023-03-04 15:44:53 +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
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
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
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
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
mrbayes
mrtrix	treewide: switch to nativeCheckInputs	2023-01-21 12:00:00 +00:00
muscle	muscle: fix pname	2023-01-28 04:20:00 +00:00
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
prodigal
quast	treewide: python{ => .pythonForBuild}.interpreter	2023-02-26 20:26:17 +00:00
raxml
repseek
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
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: fix pname	2023-01-28 04:20:00 +00:00
whisper	treewide: pkgs/applications: mark broken for darwin	2022-05-29 10:56:04 +02:00
xenomapper