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999 Commits

Author SHA1 Message Date
Felix Bühler
fb2c37b576
Merge pull request #216064 from Stunkymonkey/treewide-pname-version-1 
inormalize/minc-widgets/gimp-plugins: use pname & version
 2023-02-13 19:25:08 +01:00
Alyssa Ross
c6c7493c3b
Merge remote-tracking branch 'origin/master' into staging-next 
Conflicts:
	pkgs/development/python-modules/pyarrow/default.nix
 2023-02-13 00:15:28 +00:00
Felix Buehler
db348eb0d6 inormalize/minc-widgets/gimp-plugins: use pname & version 2023-02-12 22:21:44 +01:00
R. Ryantm
10c93d977d last: 1445 -> 1447 2023-02-12 17:14:30 +00:00
github-actions[bot]
15bfb025ab
Merge master into staging-next 2023-02-11 18:01:19 +00:00
R. Ryantm
cc7591f90e eggnog-mapper: 2.1.9 -> 2.1.10 2023-02-11 08:43:59 +00:00
github-actions[bot]
9be52f693f
Merge master into staging-next 2023-02-10 12:01:38 +00:00
R. Ryantm
b64bc146ed diamond: 2.1.0 -> 2.1.1 2023-02-10 02:56:54 +00:00
github-actions[bot]
b30088fc3f
Merge master into staging-next 2023-02-07 00:02:12 +00:00
R. Ryantm
38e3d21824 stacks: 2.60 -> 2.62 2023-02-06 21:36:49 +01:00
github-actions[bot]
b2a1140ada
Merge master into staging-next 2023-02-06 06:01:25 +00:00
R. Ryantm
0fd2901e31 varscan: 2.4.4 -> 2.4.5 2023-02-05 13:38:28 +00:00
github-actions[bot]
cb231fb28d
Merge master into staging-next 2023-02-05 06:01:18 +00:00
R. Ryantm
eadaccaa42 igv: 2.15.5 -> 2.16.0 2023-02-04 18:01:58 +00:00
github-actions[bot]
6d7be19afb
Merge master into staging-next 2023-02-02 18:01:08 +00:00
Sandro
a9cadfb7b8
Merge pull request #213490 from OPNA2608/refactor/yaml-cpp 
yaml-cpp*: Refactor, rename, adopt
 2023-02-02 17:32:34 +01:00
Vladimír Čunát
9287f4461d
Merge #206907: stdenv: gcc11 -> gcc12 2023-02-01 16:54:44 +01:00
OPNA2608
c9b4c7dccd treewide: Rename libyamlcpp* to yaml-cpp* 2023-01-31 16:22:54 +01:00
Nick Cao
c84edce4ec
Merge pull request #213063 from r-ryantm/auto-update/diamond 
diamond: 2.0.15 -> 2.1.0
 2023-01-31 16:47:56 +08:00
Mario Rodas
e5c51680fd muscle: fix pname 2023-01-28 04:20:00 +00:00
Mario Rodas
6aae8e96f8 veryfasttree: fix pname 2023-01-28 04:20:00 +00:00
github-actions[bot]
387a5e220d
Merge staging-next into staging 2023-02-28 00:03:08 +00:00
github-actions[bot]
40707bbbb3
Merge staging-next into staging 2023-02-27 18:02:06 +00:00
Sergei Trofimovich
e7e072d05a Merge remote-tracking branch 'origin/staging-next' into staging 
Conflicts:
	pkgs/top-level/python-aliases.nix

Trivial conflict of multiple added aliases.
 2023-02-26 21:53:22 +00:00
Jan Tojnar
9bb986284f Merge branch 'staging-next' into staging 
# Conflicts:
#	pkgs/development/python-modules/mdp/default.nix
#	pkgs/top-level/python-aliases.nix
 2023-02-26 01:13:37 +01:00
github-actions[bot]
3cdd771820
Merge staging-next into staging 2023-02-23 18:01:49 +00:00
github-actions[bot]
a13cd94b7b
Merge staging-next into staging 2023-02-22 00:03:12 +00:00
github-actions[bot]
fc3641aa1e
Merge staging-next into staging 2023-02-21 00:03:04 +00:00
Martin Weinelt
19697a0e67
python310Packages.xlsxwriter: Normalize attribute & dirname 2023-02-19 22:32:10 +01:00
Fabián Heredia Montiel
0cf5d85f0c treewide: add gcc12 flags 2023-01-27 21:20:52 -06:00
R. Ryantm
01c2d762f3 diamond: 2.0.15 -> 2.1.0 2023-01-28 02:58:32 +00:00
Ben Darwin
b27838807e ants: unpin vtk dependency 2023-01-27 00:21:26 -05:00
Fabian Affolter
bf0a5df606
Merge pull request #212793 from fabaff/last-fix 
last: 1422 -> 1445
 2023-01-26 20:06:44 +01:00
Fabian Affolter
e14e8f5f31 last: 1422 -> 1445 2023-01-26 16:10:25 +01:00
R. Ryantm
422b1c5144 igv: 2.15.4 -> 2.15.5 2023-01-25 17:03:16 +00:00
Justin Bedő
ed15930675
Merge pull request #211057 from r-ryantm/auto-update/last 
last: 1411 -> 1422
 2023-01-23 22:22:52 +00:00
Sandro
7726aa9ce6
Merge pull request #206287 from amesgen/add-TandemAligner 2023-01-23 23:12:36 +01:00
Weijia Wang
02d3fe6418
Merge pull request #212113 from r-ryantm/auto-update/sambamba 
sambamba: 0.8.2 -> 1.0.0
 2023-01-23 21:01:50 +01:00
Nick Cao
06d76bd44e
Merge pull request #210641 from r-ryantm/auto-update/star 
star: 2.7.10a -> 2.7.10b
 2023-01-23 16:16:01 +08:00
Weijia Wang
90e2800173
Merge pull request #198962 from r-ryantm/auto-update/bowtie2 
bowtie2: 2.4.5 -> 2.5.1
 2023-01-23 05:32:54 +01:00
Weijia Wang
6bfeb6aa68
Merge pull request #195005 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.27.4 -> 2.27.5
 2023-01-22 22:40:27 +01:00
R. Ryantm
2166bf1bfe sambamba: 0.8.2 -> 1.0.0 2023-01-22 13:54:41 +00:00
Weijia Wang
218c4c526e
Merge pull request #212002 from mothsART/feature/replace_http_by_https 
treewide: replace http by https when https is a permanent redirection
 2023-01-22 03:26:02 +01:00
Ferry Jérémie
65d7e87fdb treewide: replace http by https when https is a permanent redirection 2023-01-22 02:46:49 +01:00
R. Ryantm
2660299f54 bowtie2: 2.4.5 -> 2.5.1 2023-01-21 21:19:00 +00:00
Guillaume Girol
33afbf39f6 treewide: switch to nativeCheckInputs 
checkInputs used to be added to nativeBuildInputs. Now we have
nativeCheckInputs to do that instead. Doing this treewide change allows
to keep hashes identical to before the introduction of
nativeCheckInputs.
 2023-01-21 12:00:00 +00:00
R. Ryantm
d269d79261 last: 1411 -> 1422 2023-01-16 09:13:32 +00:00
R. Ryantm
fc65d6e66e star: 2.7.10a -> 2.7.10b 2023-01-14 06:06:52 +00:00
github-actions[bot]
33aa224777
Merge master into staging-next 2023-01-09 18:01:24 +00:00
R. Ryantm
e0db41ab1a ants: 2.4.2 -> 2.4.3 2023-01-09 09:48:53 -06:00
Robert Schütz
b3241be75d python310Packages.levenshtein: don't use alias 2023-01-09 06:09:31 -08:00
R. Ryantm
605d013aac igv: 2.15.1 -> 2.15.4 2023-01-03 14:36:54 +08:00
Ben Darwin
9c748218f2 itk: unstable -> 5.3.0 2022-12-27 09:06:37 +01:00
Sandro
b20fb264cc
Merge pull request #197575 from thyol/sratoolkit-init 2022-12-24 02:58:47 +01:00
amesgen
d499bc2447
tandem-aligner: init at unstable-2022-09-17 2022-12-15 20:48:53 +01:00
Weijia Wang
fa19b16e93 ecopcr: 0.8.0 -> 1.0.1 2022-12-08 04:35:53 +01:00
Jonas Heinrich
20193b6d86
Merge pull request #202395 from thyol/muscle 
muscle: 3.8.31 -> 5.1.0
 2022-11-24 15:47:12 +01:00
Jonas Heinrich
57728b51cf
Merge pull request #202404 from thyol/veryfasttree 
veryfasttree: init at 3.1.1
 2022-11-24 15:14:13 +01:00
thyol
cdcb7946ba veryfasttree: init at 3.1.1 2022-11-22 20:45:45 +01:00
thyol
35d3a6fa79 muscle: add myself to maintainers 2022-11-22 20:19:17 +01:00
thyol
d7c8595f62 muscle: 3.8.31 -> 5.1.0 2022-11-22 20:19:17 +01:00
thyol
81d6f1c7dc sratoolkit: init at 2.11.3 2022-11-21 20:27:28 +01:00
R. Ryantm
6ba0d20487 igv: 2.14.1 -> 2.15.1 2022-11-20 14:06:29 +08:00
Jiajie Chen
fc2812a1f8 nest: init at 3.3 2022-11-10 09:20:41 +08:00
R. Ryantm
c7ba9b459c delly: 1.1.5 -> 1.1.6 2022-11-08 18:21:37 +00:00
Justin Bedő
3a90ab68e6
Merge pull request #197631 from jbedo/octopus 
octopus-caller: backport patch to fix build
 2022-11-07 21:26:21 +00:00
Bruno Bzeznik
9243a44c9c seqkit: init at 2.3.1 2022-11-04 08:51:32 +01:00
Stanisław Pitucha
9ed8ce7ff3
Merge pull request #198609 from natsukium/mmseqs2/init 
mmseqs2: init at 14-7e284
 2022-11-01 21:47:20 +11:00
natsukium
ed7511ad02
mmseqs2: init at 14-7e284 2022-10-31 23:49:10 +09:00
Justin Bedo
5f5bb45093
octopus-caller: backport patch to fix build 2022-10-25 09:52:28 +11:00
OPNA2608
982a1bfd80 sambamba: fix compilation on Darwin, cleanup installPhase 2022-10-23 16:12:47 +02:00
Jan Tojnar
457f28f6f8 Merge branch 'master' into staging-next 
; Conflicts:
;	pkgs/development/tools/codespell/default.nix

codespell 2.2.2 switched to pyproject & setuptools_scm:
https://github.com/codespell-project/codespell/pull/2523
 2022-10-19 05:24:28 +02:00
R. Ryantm
4ab06e3223 ants: 2.4.1 -> 2.4.2 2022-10-19 09:19:31 +08:00
github-actions[bot]
f52955a521
Merge master into staging-next 2022-10-16 18:01:42 +00:00
R. Ryantm
00b3b4ee24 gatk: 4.2.6.1 -> 4.3.0.0 2022-10-16 21:48:30 +08:00
Martin Weinelt
51fcbf5bb7 Merge remote-tracking branch 'origin/master' into staging-next 2022-10-16 00:18:40 +02:00
Jonas Heinrich
9259c4b841
Merge pull request #195990 from r-ryantm/auto-update/angsd 
angsd: 0.938 -> 0.940
 2022-10-15 09:33:23 +02:00
github-actions[bot]
886633ba43
Merge master into staging-next 2022-10-15 00:04:00 +00:00
R. Ryantm
4cee9b9ddb angsd: 0.938 -> 0.940 2022-10-14 14:50:26 +00:00
Artturi
e66d2fd89d
Merge pull request #194256 from Artturin/treewides2 2022-10-13 00:08:01 +03:00
Markus S. Wamser
c9d167f174 pkgs.applications: remove unused args 2022-10-12 16:00:16 +02:00
Martin Weinelt
cf7f4393f3
Merge pull request #193494 from NixOS/staging-next 2022-10-11 01:12:59 +02:00
Alexis Praga
2ce78bd571 gatk: add java and python to PATH 
gatk is actually a python script that starts either the local or spark
.jar file according to a fixed setup.
In the initial commit, neither java nor python were present in PATH.
 2022-10-10 23:06:01 +02:00
Artturin
7e49471316 treewide: optional -> optionals where the argument is a list 
the argument to optional should not be list
 2022-10-10 15:40:21 +03:00
R. Ryantm
92bc5dbbae picard-tools: 2.27.4 -> 2.27.5 2022-10-08 00:09:59 +00:00
github-actions[bot]
f18d801779
Merge staging-next into staging 2022-09-28 18:05:53 +00:00
R. Ryantm
ddf9f1800a delly: 1.1.3 -> 1.1.5 2022-09-27 11:26:09 +00:00
Artturin
0734f54ef2 treewide: move pkg-config, autoreconfHook, intltool to nativeBuildInputs 
found with nixpkgs-lint
 2022-09-26 17:53:26 +03:00
Justin Bedő
d21b5ac044
Merge pull request #192211 from r-ryantm/auto-update/last 
last: 1409 -> 1411
 2022-09-26 11:49:30 +10:00
Brad Langhorst
2beb26b45b seqtk: init at 1.3 
Co-authored-by: Anderson Torres <torres.anderson.85@protonmail.com>
 2022-09-25 19:55:58 -04:00
R. Ryantm
1008651931 last: 1409 -> 1411 2022-09-21 08:24:01 +00:00
Christian Kögler
e06e88d003
Merge pull request #189923 from r-ryantm/auto-update/igv 
igv: 2.14.0 -> 2.14.1
 2022-09-18 15:59:16 +02:00
R. Ryantm
9da745bfaf messer-slim: 4.0 -> 4.0.1 2022-09-15 22:25:51 +00:00
Sandro
785031e430
Merge pull request #185819 from apraga/gatk-4.2.6.1 2022-09-10 21:31:42 +02:00
natsukium
9e65d09e3d
mafft: 7.505 -> 7.508 
changed to fetch from new gitlab repository
 2022-09-09 13:26:38 +09:00
R. Ryantm
c7832514ef igv: 2.14.0 -> 2.14.1 2022-09-05 22:29:15 +00:00
Sandro
ef987a9604
Merge pull request #189329 from bcdarwin/itk4-removal 2022-09-05 16:05:51 +02:00
Sandro
73bf7a0ca0
Merge pull request #181954 from bzizou/treemix 2022-09-05 15:57:48 +02:00
Bruno Bzeznik
7c09cfdc1a treemix: init at 1.13 2022-09-05 06:55:03 +02:00
Jonas Heinrich
eb3d3b2e90
Merge pull request #175449 from bzizou/iqtree 
iqtree: init at 2.2.0.4
 2022-09-04 23:58:04 +02:00
Ben Darwin
1280129aab EZminc: itk4 -> itk (formally; package is broken) 2022-09-04 13:36:24 -04:00
Ben Darwin
961b308fe1 ants: 2.2.0 -> 2.4.1 2022-09-04 13:36:24 -04:00
Alexis Praga
95da303902 gatk : init at 4.2.6.1 
GATK is the industry standard for genetics analysis, more precisely for
identifying SNPs and indels in germline DNA and RNAseq data .
This package does not ship the Spark version.

Apply suggestions from code review
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
 2022-09-04 15:34:30 +02:00
Jonas Heinrich
3b3a01e3f9
Merge pull request #188785 from jbedo/last 
last: 1406 -> 1409
 2022-09-04 12:40:30 +02:00
Justin Bedo
d9acf90371
last: 1406 -> 1409 2022-09-04 10:36:01 +10:00
Sandro
9b214e6dad
Merge pull request #177830 from r-ryantm/auto-update/eggnog-mapper 2022-09-03 22:43:11 +02:00
Jonas Heinrich
ed227dc9fb
Merge pull request #168109 from r-ryantm/auto-update/bcftools 
bcftools: 1.15 -> 1.16
 2022-08-27 08:51:34 +02:00
Jonas Heinrich
21ba29f226
Merge pull request #181338 from thyol/diamond 
diamond: 0.8.36 -> 2.0.15
 2022-08-25 15:25:03 +02:00
Jonas Heinrich
b8e0c9b652
Merge pull request #183253 from r-ryantm/auto-update/angsd 
angsd: 0.937 -> 0.938
 2022-08-24 10:35:05 +02:00
Jonas Heinrich
c199cfabff
Merge pull request #184694 from r-ryantm/auto-update/SPAdes 
SPAdes: 3.15.4 -> 3.15.5
 2022-08-23 20:21:42 +02:00
Jonas Heinrich
5cb64f6046
Merge pull request #186958 from r-ryantm/auto-update/igv 
igv: 2.13.2 -> 2.14.0
 2022-08-21 21:11:49 +02:00
R. Ryantm
49f4071f30 eggnog-mapper: 2.1.7 -> 2.1.9 2022-08-21 12:45:21 +00:00
Jonas Heinrich
8508d5decf
Merge pull request #183724 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.26.11 -> 2.27.4
 2022-08-21 10:03:42 +02:00
R. Ryantm
98d1f4c35d bcftools: 1.15 -> 1.16 2022-08-18 18:44:42 +00:00
R. Ryantm
f4c3ff2d7f igv: 2.13.2 -> 2.14.0 2022-08-16 13:24:02 +00:00
R. Ryantm
c37112d2d0 messer-slim: 3.7.1 -> 4.0 2022-08-14 14:11:37 +00:00
Mario Rodas
0cab4c8f8a
Merge pull request #183012 from bcdarwin/update-mni-autoreg 
mni_autoreg: unstable-2017-09-22 -> unstable-2022-05-20
 2022-08-13 01:05:26 -05:00
Mario Rodas
6aeb44c32e
Merge pull request #185211 from r-ryantm/auto-update/delly 
delly: 1.0.3 -> 1.1.3
 2022-08-13 00:41:48 -05:00
kilianar
0442ab82e0 igv: 2.8.13 -> 2.13.2 
- https://software.broadinstitute.org/software/igv/2.9.x
- https://software.broadinstitute.org/software/igv/2.10.x
- https://software.broadinstitute.org/software/igv/2.11.x
- https://software.broadinstitute.org/software/igv/2.12.x
- https://software.broadinstitute.org/software/igv/2.13.x
 2022-08-07 17:53:06 +02:00
Bobby Rong
934c6c9a95
Merge pull request #184334 from r-ryantm/auto-update/mafft 
mafft: 7.490 -> 7.505
 2022-08-07 16:18:05 +08:00
R. Ryantm
8b7c09d0e6 delly: 1.0.3 -> 1.1.3 2022-08-05 08:58:15 +00:00
Sandro
e9984bc607
Merge pull request #182705 from luispedro/no_test_samtools_on_cross_compile 2022-08-02 23:20:38 +02:00
Luis Pedro Coelho
5877d8e072 samtools: Fix cross-compilation 
Tests require bgzip which comes from the htslib package.

This did not cause problems prior to
41485e7337 as tests were not run in
cross-compilation.
 2022-08-02 17:52:50 +02:00
Sandro
e76aa82431
Merge pull request #184598 from wegank/treewide-fix-platforms 2022-08-02 15:57:56 +02:00
R. Ryantm
921b81745d SPAdes: 3.15.4 -> 3.15.5 2022-08-02 02:26:56 +00:00
Weijia Wang
278086eddb treewide: fix platforms 2022-08-01 18:33:27 +02:00
R. Ryantm
b2bbba02ba mafft: 7.490 -> 7.505 2022-07-31 20:32:57 +00:00
R. Ryantm
e0a9011556 last: 1268 -> 1406 2022-07-31 16:58:20 +00:00
R. Ryantm
9338d8c9b7 picard-tools: 2.26.11 -> 2.27.4 2022-07-29 16:12:10 +00:00
R. Ryantm
8c0e56fc14 angsd: 0.937 -> 0.938 2022-07-28 07:50:11 +00:00
Justin Bedő
9e80da74b0
Merge pull request #182028 from jbedo/bedops 
bedops: 2.4.40 -> 2.4.41
 2022-07-28 09:14:23 +10:00
Ben Darwin
125da19866 mni_autoreg: unstable-2017-02-22 -> unstable-2022-05-20 2022-07-26 16:03:12 -04:00
natsukium
cf0dc604a6
dssp: init at 4.0.5 2022-07-19 12:17:34 +09:00
Justin Bedo
99fb9abfaa
bedops: 2.4.40 -> 2.4.41 2022-07-19 09:09:52 +10:00
Lassulus
01853c3bcc
Merge pull request #174547 from r-ryantm/auto-update/delly 
delly: 0.9.1 -> 1.0.3
 2022-07-16 10:49:50 +02:00
Pascal Wittmann
26ddf3454a
Merge pull request #138255 from natsukium/mafft/init 
mafft: init at 7.487
 2022-07-16 00:54:59 +02:00
thyol
0d6e3afdba diamond: update metadata 2022-07-13 12:33:33 +02:00
thyol
55853ae096 maintainers: add thyol 2022-07-13 12:30:44 +02:00
thyol
4e79b5e370 diamond: remove patch 2022-07-13 11:58:39 +02:00
thyol
5e765ecc68 diamond: 0.8.36 -> 2.0.15 2022-07-13 11:58:02 +02:00
R. Ryantm
5ea1c721e1 delly: 0.9.1 -> 1.0.3 2022-07-07 22:10:48 +00:00
ajs124
3b5f125515 maintainers: remove metabar 
no github account + only commit is 78c052e91a
 2022-06-29 00:52:13 +02:00
Robert Scott
466c2e342a treewide/applications: add sourceType binaryNativeCode for many packages 2022-06-23 18:38:19 +01:00
Robert Scott
444d3a825a treewide/python-modules: add sourceProvenance for several packages 2022-06-20 09:43:10 +02:00
Sandro Jäckel
0f14467d44
MACS2: mark broken 2022-06-06 11:46:22 -07:00
Robert Scott
3b6bc4b69c treewide: set sourceProvenance for packages containing downloaded jars 
these are the easily identifiable cases and will not be comprehensive
 2022-06-04 19:47:57 +01:00
Sergei Trofimovich
fd48676596
Merge pull request #175259 from trofi/workaround-fno-common-for-svaba 
svaba: add -fcommon workaround
 2022-06-03 05:59:16 +00:00
ckie
958fcfb4fa
Merge pull request #175477 from bzizou/astral 
astral: init at 5.7.1
 2022-05-31 14:55:37 +03:00
Bruno Bzeznik
376897ced3 astral: init at 5.7.1 2022-05-31 09:03:24 +02:00
Rick van Schijndel
433701147a
treewide: pkgs/applications: mark broken for aarch64-linux 2022-05-30 13:42:58 +02:00