Ben Darwin 5cf446f41b ezminc: mark broken ... Package refuses to build with current GCC (11), but building with older GCC causes error linking libminc and I don't want to pin a bunch of deps. A newer version is available upstream but it only works with ITK 5.0 (see https://github.com/BIC-MNI/EZminc/issues/15), but we have 4.x and 5.2.x in tree and I'm reluctant to add 5.0 just for one package (even ITK 4.x is only used by ants and ezminc and should be removed as soon as ants is upgraded).		2022-05-17 10:24:07 -07:00
..
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
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
bftools
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
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
exonerate
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
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
inormalize
itsx
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
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
macse	treewide: convert phases that contain ":" to dont* = true (#130500)	2021-07-18 23:42:48 +02:00
manta
megahit	Static build for megahit	2022-05-04 02:13:31 +02:00
meme-suite
messer-slim	messer-slim: 3.7 -> 3.7.1	2022-02-14 00:46:29 +00:00
migrate
minc-tools
minc-widgets
minia
minimap2	minimap2: enable aarch64 builds (#161169)	2022-03-04 12:27:29 +01:00
mni_autoreg
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
N3
neuron	neuron-mpi: remove appendToName to have a consistent package name for repology	2022-02-28 12:46:15 +01:00
niftyreg
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
paml
picard-tools	treewide: add meta.mainProgram to many packages	2022-04-14 10:24:01 -07:00
platypus
plink-ng
poretools	python,pythonPackages: make aliases	2022-01-16 18:39:59 +00:00
prodigal
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
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
somatic-sniper
sortmerna
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
subread	subread: init 2.0.3	2021-12-14 13:30:23 +11:00
sumatools
svaba
tebreak	treewide: remove nativeBuildInputs that are in stdenv	2022-04-16 21:46:46 +03:00
trimal
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
whisper
xenomapper	python3Packages.xenomapper: move to top-level	2022-01-01 02:09:11 +01:00