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1004 Commits

Author SHA1 Message Date
Robert Scott
2107f7de60
Merge pull request #225865 from bzizou/samtools 
samtools: 1.13 -> 1.17
 2023-04-13 00:10:42 +01:00
Bruno Bzeznik
d69d242b7b Samtools: 1.13 -> 1.17 
Changelogs:
 - https://github.com/samtools/samtools/releases/tag/1.14
 - https://github.com/samtools/samtools/releases/tag/1.15
 - https://github.com/samtools/samtools/releases/tag/1.15.1
 - https://github.com/samtools/samtools/releases/tag/1.16
 - https://github.com/samtools/samtools/releases/tag/1.16.1
 - https://github.com/samtools/samtools/releases/tag/1.17
 2023-04-12 12:00:25 +02:00
natsukium
f962206f94
mafft: 7.515 -> 7.520 
https://gitlab.com/sysimm/mafft/-/tags/v7.520
 2023-04-12 13:28:24 +09:00
R. Ryantm
8fcdc3f62c varscan: 2.4.5 -> 2.4.6 2023-04-05 14:55:31 +00:00
Weijia Wang
150dcd7ce7
Merge pull request #224345 from natsukium/blast/darwin 
blast-bin: init at 2.13.0
 2023-04-03 09:59:08 +03:00
natsukium
cddb4a24ba
blast-bin: init at 2.13.0 2023-04-03 12:39:17 +09:00
Justin Bedo
e739dc5088
last: 1447 -> 1453 2023-04-03 08:38:27 +10:00
github-actions[bot]
cead7e3e73
Merge master into staging-next 2023-03-25 00:02:20 +00:00
Weijia Wang
2ce97f2bf9
Merge pull request #222464 from r-ryantm/auto-update/diamond 
diamond: 2.1.5 -> 2.1.6
 2023-03-24 20:56:17 +02:00
github-actions[bot]
0537539006
Merge master into staging-next 2023-03-22 12:01:22 +00:00
Nick Cao
6c4095e7af
Merge pull request #222331 from r-ryantm/auto-update/seqkit 
seqkit: 2.3.1 -> 2.4.0
 2023-03-22 16:08:39 +08:00
R. Ryantm
4c2324cf14 diamond: 2.1.5 -> 2.1.6 2023-03-22 03:09:40 +00:00
R. Ryantm
a6f33bd62f seqkit: 2.3.1 -> 2.4.0 2023-03-21 10:45:22 +00:00
Martin Weinelt
9959ec97f8
Merge remote-tracking branch 'origin/master' into staging-next 
Conflicts:
- pkgs/development/python-modules/wxPython/4.0.nix
- pkgs/development/python-modules/wxPython/4.1.nix
 2023-03-20 15:07:36 +01:00
Weijia Wang
802b7ac3e7
Merge pull request #221743 from r-ryantm/auto-update/gatk 
gatk: 4.3.0.0 -> 4.4.0.0
 2023-03-20 14:33:37 +02:00
github-actions[bot]
84c97a9e91
Merge master into staging-next 2023-03-19 18:00:59 +00:00
natsukium
21affa5ff1
trf: init at 4.09.1 2023-03-19 22:25:42 +09:00
github-actions[bot]
c70342c89c
Merge master into staging-next 2023-03-19 00:02:27 +00:00
Weijia Wang
7574e25ef3
Merge pull request #221864 from natsukium/mafft/update 
mafft: 7.508 -> 7.515
 2023-03-19 00:03:19 +02:00
github-actions[bot]
403b148aa5
Merge master into staging-next 2023-03-18 18:01:02 +00:00
natsukium
f3b75ef3ce
mafft: 7.508 -> 7.515 2023-03-19 00:42:29 +09:00
Fabian Affolter
109f8ccdfe
nest: specify license 2023-03-18 11:23:52 +01:00
Fabian Affolter
c7ec291235
nest: add changelog to meta 2023-03-18 11:23:06 +01:00
Weijia Wang
ea847dd1a0 nest: 3.3 -> 3.4 2023-03-18 12:13:46 +02:00
R. Ryantm
0d44f838ca gatk: 4.3.0.0 -> 4.4.0.0 2023-03-18 01:10:14 +00:00
github-actions[bot]
f5629a4518
Merge master into staging-next 2023-03-17 06:01:16 +00:00
R. Ryantm
2a35b86739 subread: 2.0.3 -> 2.0.4 2023-03-16 23:09:44 +00:00
Vladimír Čunát
0f9354bfee
Merge #218309: ffmpeg: ffmpeg_4 → ffmpeg_5 
...into staging
 2023-03-16 11:11:31 +01:00
Martin Weinelt
6b67186fe9
Merge remote-tracking branch 'origin/master' into staging-next 
Conflicts:
- pkgs/development/python-modules/crownstone-cloud/default.nix
- pkgs/development/python-modules/exrex/default.nix
- pkgs/development/python-modules/mkdocs-minify/default.nix
- pkgs/development/python-modules/myjwt/default.nix
- pkgs/development/tools/analysis/checkov/default.nix
 2023-03-14 08:14:26 +01:00
Artturi
b978bf0f0f
Merge pull request #220570 from Artturin/fixlints1 2023-03-14 02:15:55 +02:00
Atemu
9bd2506458 treewide: make ffmpeg_4-dependant packages depend on ffmpeg_4 
These packages were identified as broken when ffmpeg = ffmpeg_5.

Tested _only_ by building them. If you are a maintainer of one of these
packages, please test whether your package still works.
 2023-03-13 16:42:22 -06:00
Vladimír Čunát
1dd94ad62f
Merge branch 'master' into staging-next 2023-03-12 09:06:28 +01:00
R. Ryantm
77c83ddbc9 diamond: 2.1.4 -> 2.1.5 2023-03-11 18:22:58 +00:00
Artturin
cab4a24c34 treewide: fix lints 
Arg to lib.optional is a list

build time tool in buildInputs
 2023-03-11 00:55:17 +02:00
Martin Weinelt
8a085cd8e3 Merge remote-tracking branch 'origin/master' into staging-next 2023-03-05 15:36:16 +01:00
R. Ryantm
e175a2ea68 diamond: 2.1.3 -> 2.1.4 2023-03-04 15:44:53 +00:00
Martin Weinelt
d0286ecd24 Merge remote-tracking branch 'origin/staging' into staging-next 2023-03-04 01:42:06 +00:00
R. Ryantm
99785ee90e picard-tools: 2.27.5 -> 3.0.0 2023-03-01 14:43:38 +00:00
Weijia Wang
ccd9d6da1e
Merge pull request #218118 from r-ryantm/auto-update/diamond 
diamond: 2.1.1 -> 2.1.3
 2023-02-27 21:28:18 +02:00
Artturi
1c6a1e5650
Merge pull request #218500 from alyssais/pythonForBuild 2023-02-27 18:17:27 +02:00
Weijia Wang
21bb99733d
Merge pull request #218342 from r-ryantm/auto-update/bcftools 
bcftools: 1.16 -> 1.17
 2023-02-27 18:02:55 +02:00
Alyssa Ross
2bfa93e01c
treewide: python{ => .pythonForBuild}.interpreter 
It won't be enough to fix cross in all cases, but it is in at least
one: pywayland.  I've only made the change in cases I'm confident it's
correct, as it would be wrong to change this when python.interpreter
is used in wrappers, and possibly when it's used for running tests.
 2023-02-26 20:26:17 +00:00
R. Ryantm
f2465e1ecf neuron-full: 8.2.1 -> 8.2.2 2023-02-26 05:18:37 +00:00
R. Ryantm
95ca5f576c bcftools: 1.16 -> 1.17 2023-02-25 23:02:27 +00:00
Weijia Wang
c8ba046415
Merge pull request #217897 from DavidCromp/nest 
nest: fix Python & Darwin
 2023-02-25 19:47:22 +02:00
DavidCromp
5ce4a02687 nest: fix Python & Darwin 
Removed auto-patch-elf and replaced with find command that moves
libraries where they are expected by nest. Auto-patchelf isn't
supported on aarch64, so I copied my local derivation fix I've been
using.

PyNEST also requires numpy, so that has been added to
propagatedbuildinputs.

Also added support for OpenMP on Darwin.
 2023-02-25 10:28:59 -05:00
Artturi
8e027ec1d1
Merge pull request #218240 from amesgen/tandem-aligner-fix-build-gcc-12 2023-02-25 15:35:12 +02:00
amesgen
a85b73c514
tandem-aligner: fix build with GCC 12 2023-02-25 13:40:11 +01:00
R. Ryantm
60ee2eaf54 diamond: 2.1.1 -> 2.1.3 2023-02-24 23:46:09 +00:00
Artturin
f9fdf2d402 treewide: move NIX_CFLAGS_COMPILE to the env attrset 
with structuredAttrs lists will be bash arrays which cannot be exported
which will be a issue with some patches and some wrappers like cc-wrapper

this makes it clearer that NIX_CFLAGS_COMPILE must be a string as lists
in env cause a eval failure
 2023-02-22 21:23:04 +02:00
Artturin
6f6cc4a22d treewide: use toString on list NIX_CFLAGS_COMPILE 
with structuredAttrs lists will be bash arrays which cannot be exported
which will be a issue with some patches and some wrappers like cc-wrapper
 2023-02-22 21:23:04 +02:00
DavidCrompton1192@gmail.com
77aed40027 neuron: 7.5 -> 8.2.1 2023-02-21 13:52:34 -05:00
Ferry Jérémie
bfac2d0034 treewide:replace http by https when https is a permanent redirection 2023-02-19 21:47:59 +01:00
Sandro
ab78a72cd0
Merge pull request #198872 from jiegec/nest 
nest: init at 3.3
 2023-02-17 13:53:52 +01:00
Felix Buehler
cdb39a86e0 treewide: use optionalString 2023-02-13 21:52:34 +01:00
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