Bruno Bzeznik
1ba3f3f00f
SPAdes: init at 3.13.1 ( #63082 )
2019-10-03 09:18:48 +00:00
Ryan Mulligan
8519cd1aa0
Merge pull request #69735 from r-ryantm/auto-update/picard-tools
...
picard-tools: 2.20.5 -> 2.20.8
2019-09-29 15:44:33 -07:00
R. RyanTM
de95a92384
star: 2.7.1a -> 2.7.2b
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/star/versions
2019-09-28 21:09:40 -07:00
R. RyanTM
8c397c2bc2
picard-tools: 2.20.5 -> 2.20.8
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
2019-09-27 18:25:22 -07:00
Aaron Andersen
af5176b430
Merge pull request #63117 from bzizou/macse
...
macse: init at 2.03
2019-09-27 17:26:07 -04:00
Bruno Bzeznik
e4108becbe
macse: init at 2.03
2019-09-24 08:24:07 +02:00
Miguel Madrid Mencía
148c82e07e
maintainer: mimadrid: update github username and personal data
2019-09-14 12:15:46 +02:00
Linus Heckemann
f6182da2c6
ants: use itk 4.x
2019-09-13 11:54:21 +02:00
volth
7b8fb5c06c
treewide: remove redundant quotes
2019-09-08 23:38:31 +00:00
Frederik Rietdijk
5f4734b1dd
Merge remote-tracking branch 'upstream/gcc-8' into staging-next
...
Earlier the gcc8 branch was merged instead of the gcc-8 branch (note the dash)...
2019-09-08 20:44:26 +02:00
Frederik Rietdijk
66bc7fc1b3
Merge master into staging-next
2019-09-06 22:46:05 +02:00
Justin Bedo
6beabe7d2c
bedtools: 2.28.0 -> 2.29.0
2019-09-06 21:23:15 +02:00
Jan Tojnar
cdf426488b
Merge branch 'master' into staging-next
...
Fixed trivial conflicts caused by removing rec.
2019-09-06 03:20:09 +02:00
Justin Bedo
3f83cbf538
xenomapper: init 1.0.2
2019-09-05 20:50:22 +10:00
Franz Pletz
de85797565
Merge remote-tracking branch 'origin/master' into gcc-8
2019-09-03 22:15:07 +02:00
Vladimír Čunát
f21211ebfe
Merge branch 'master' into staging
2019-09-02 23:25:24 +02:00
Tadeo Kondrak
2aa9b655f4
kallisto: 0.43.1 -> 0.46.0
2019-08-31 14:06:31 -06:00
Frederik Rietdijk
98ef78326d
Merge staging-next into staging
2019-08-31 18:07:33 +02:00
Frederik Rietdijk
96e5474329
Merge master into staging-next
2019-08-31 18:04:31 +02:00
Lassulus
a8d26fc34a
Merge pull request #63127 from bzizou/trimal
...
trimal: init at 1.4.1
2019-08-31 13:04:41 +02:00
Frederik Rietdijk
ad1d58c622
Merge staging-next into staging
2019-08-31 10:04:20 +02:00
Frederik Rietdijk
fc74ba8291
Merge master into staging-next
2019-08-31 09:50:38 +02:00
volth
08f68313a4
treewide: remove redundant rec
2019-08-28 11:07:32 +00:00
Léo Gaspard
8a4721d606
Merge pull request #64669 from luispedro/add_sortmerna
...
sortmerna: init at 3.0.3
2019-08-27 17:19:53 +02:00
Luis Pedro Coelho
bc22c2e07f
sortmerna: init at 3.0.3
...
This is a useful package in bioinformatics, namely in processing
short-read sequencing data from metagenomes
2019-08-27 00:37:43 +02:00
Robin Gloster
616b8343c4
Merge remote-tracking branch 'upstream/master' into gcc-8
2019-08-25 18:55:46 +02:00
Vladimír Čunát
2e6bf42a22
Merge branch 'master' into staging-next
...
There ver very many conflicts, basically all due to
name -> pname+version. Fortunately, almost everything was auto-resolved
by kdiff3, and for now I just fixed up a couple evaluation problems,
as verified by the tarball job. There might be some fallback to these
conflicts, but I believe it should be minimal.
Hydra nixpkgs: ?compare=1538299
2019-08-24 08:55:37 +02:00
R. RyanTM
41571dc81a
picard-tools: 2.20.4 -> 2.20.5
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
2019-08-19 21:40:40 -07:00
volth
46420bbaa3
treewide: name -> pname (easy cases) ( #66585 )
...
treewide replacement of
stdenv.mkDerivation rec {
name = "*-${version}";
version = "*";
to pname
2019-08-15 13:41:18 +01:00
R. RyanTM
3bfd09b76d
picard-tools: 2.20.3 -> 2.20.4
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
2019-08-04 23:04:42 -07:00
Robin Gloster
c6f1c9044b
Merge pull request #63282 from jbedo/strelka
...
strelka: 2.9.5 -> 2.9.10
2019-08-01 23:44:58 +00:00
lewo
481bb449a2
Merge pull request #64897 from bzizou/est-sfs
...
est-sfs: init at 2.03
2019-07-22 22:52:16 +02:00
Justin Bedo
11ed86d873
bedtools: 2.27.1 -> 2.28.0
2019-07-20 14:15:38 +02:00
R. RyanTM
9a6f0ca8b7
stacks: 2.4 -> 2.41
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/stacks/versions
2019-07-17 09:34:10 +02:00
Ryan Mulligan
e7920cbcfc
Merge pull request #64862 from r-ryantm/auto-update/picard-tools
...
picard-tools: 2.20.2 -> 2.20.3
2019-07-16 20:04:43 -07:00
Bruno Bzeznik
9a22c8c697
est-sfs: init at 2.03
2019-07-16 13:55:59 +02:00
R. RyanTM
b7fc14d8e6
picard-tools: 2.20.2 -> 2.20.3
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
2019-07-15 21:46:51 -07:00
worldofpeace
7ce0cc0a6a
Merge pull request #64324 from jbedo/hisat2
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hisat2: fix missing perl dependency
2019-07-13 13:21:11 -04:00
Ryan Mulligan
508ae42a0f
treewide: fix redirect URLs
2019-07-10 12:52:51 -07:00
Justin Bedo
d2d449cea5
hisat2: fix missing perl dependency
2019-07-05 10:29:51 +10:00
markuskowa
a07d045b00
Merge pull request #63488 from jbedo/octopus
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octopus: init 0.6.3-beta
2019-06-27 12:43:25 +02:00
royneary
d162165350
mosdepth: 0.2.3 -> 0.2.6
2019-06-22 22:41:59 +02:00
Justin Bedo
b8b71aaaf9
octopus: init 0.6.3-beta
2019-06-19 23:09:33 +10:00
Linus Heckemann
2458209c3e
dcm2niix: 1.0.20170130 -> 1.0.20190410
2019-06-18 22:12:40 +02:00
Justin Bedo
1be8ba08d3
strelka: 2.9.5 -> 2.9.10
2019-06-17 16:09:25 +10:00
Franz Pletz
394bee72db
ants: fix build with gcc8
2019-06-17 07:26:00 +02:00
volth
f3282c8d1e
treewide: remove unused variables ( #63177 )
...
* treewide: remove unused variables
* making ofborg happy
2019-06-16 19:59:05 +00:00
Bruno Bzeznik
aafffb2614
trimal: init at 1.4.1
2019-06-14 16:31:39 +02:00
Aaron Andersen
4cb64dba39
Merge pull request #58362 from bzizou/cd-hit
...
cd-hit: init at 4.8.1
2019-06-13 20:39:54 -04:00
Bruno Bzeznik
9fbf8625f1
cd-hit: init at 4.8.1
2019-06-13 14:35:13 +02:00
Robert Scott
48c8756157
pythonPackages.neuron: restrict to x86 platforms
2019-06-09 12:18:58 +02:00
Robert Scott
e0aec554eb
pythonPackages.neuron: fix for darwin
...
un-compensate for some of the darwin quirks the neuron
source is expecting
2019-06-09 12:18:58 +02:00
R. RyanTM
8ebf0eefbe
star: 2.7.0f -> 2.7.1a ( #62577 )
...
* star: 2.7.0f -> 2.7.1a
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/star/versions
* star: cleanup
2019-06-06 18:10:34 +02:00
Matthew Bauer
d598eca41e
Merge pull request #62752 from matthewbauer/darwin-fixes100
...
Fixes for x86_64-darwin failures on Hydra
2019-06-06 09:46:41 -04:00
Matthew Bauer
441485af66
iv: only use patchelf on linux
2019-06-05 23:42:58 -04:00
R. RyanTM
2998ac28b4
picard-tools: 2.19.2 -> 2.20.2
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
2019-06-02 05:31:59 -07:00
Ryan Mulligan
34e8f3b119
Merge pull request #61997 from r-ryantm/auto-update/stacks
...
stacks: 2.3e -> 2.4
2019-05-24 06:31:43 -07:00
R. RyanTM
f4a20199d2
stacks: 2.3e -> 2.4
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/stacks/versions
2019-05-24 03:50:06 -07:00
Robin Gloster
43aa2e30c3
Merge pull request #58369 from bzizou/clustalo
...
clustal-omega: init at 1.2.4
2019-05-18 10:16:43 +00:00
Renaud
bf4728cb40
eggnog-mapper: fix patch URL and hash
2019-05-13 16:00:07 +02:00
R. RyanTM
ad5676f8b9
minimap2: 2.16 -> 2.17
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/minimap2/versions
2019-05-11 21:12:42 -07:00
Frederik Rietdijk
155c9d8e18
Merge master into staging-next
2019-05-02 08:43:14 +02:00
R. RyanTM
d41da19c65
picard-tools: 2.19.0 -> 2.19.2
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
2019-05-01 17:49:08 -07:00
Frederik Rietdijk
f137783927
Merge master into staging-next
2019-05-01 11:45:46 +02:00
R. RyanTM
cc82f81d9a
bowtie2: 2.3.5 -> 2.3.5.1
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/bowtie2/versions
2019-05-01 11:17:16 +02:00
Matthew Bauer
a3990c9f6d
Merge pull request #60447 from matthewbauer/macos-10-12-fixups
...
Fixup from macos-10-12 branch
2019-04-30 10:06:45 -04:00
Frederik Rietdijk
3462fe27d9
Merge staging-next into staging
2019-04-30 15:52:19 +02:00
Matthew Bauer
74c784a79c
treewide: make -Wno-error flags clang-only
...
In 724e833ea2
, I was a little too aggressive in enabling these flags.
Many don’t work in gcc, and we should probably avoid settings them
widely. This makes those flags optional on isclang
2019-04-29 21:34:24 -04:00
Bruno Bzeznik
83886b3d91
aragorn: init at 1.2.38 ( #58354 )
2019-04-29 07:18:03 -04:00
Matthew Bauer
87944c3125
Merge pull request #56744 from matthewbauer/macos-10-12
...
Update macOS to 10.12
2019-04-26 22:20:03 -04:00
Matthew Bauer
724e833ea2
treewide: disable -Werror for llvm 7
...
Some of these have errors on newest llvm. It’s easiest to just add
-Wno-error in these cases.
2019-04-26 21:55:04 -04:00
Renaud
71c6157fd7
Merge pull request #58534 from bzizou/sumatools.dev
...
sumatools: init at 1.0.34
2019-04-24 22:34:35 +02:00
R. RyanTM
0dc3184871
picard-tools: 2.18.27 -> 2.19.0 ( #59634 )
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
2019-04-20 13:15:40 +02:00
Aaron Andersen
11cf1a282d
Merge pull request #58377 from bzizou/exonerate
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exonerate: init at 2.4.0
2019-04-19 13:25:49 -04:00
Bruno Bzeznik
6a8c9bff8f
exonerate: init at 2.4.0
2019-04-19 14:58:57 +02:00
Bruno Bzeznik
90b4796c60
sumatools: init at 1.0.34
2019-04-19 14:43:40 +02:00
Luis Pedro Coelho
3fc55eec05
Prodigal: init at 2.6.3
2019-04-19 08:38:14 +02:00
R. RyanTM
d11731130d
star: 2.7.0c -> 2.7.0f
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/star/versions
2019-04-16 18:30:49 +02:00
Luis Pedro Coelho
13a1f2c296
eggnog-mapper: init at 1.0.3 ( #58905 )
2019-04-14 17:22:47 -07:00
Frederik Rietdijk
4a125f6b20
Merge master into staging-next
2019-04-07 08:33:41 +02:00
Pascal Wittmann
cfb6ade58c
Merge pull request #58931 from bzizou/migrate
...
migrate: init at 3.7.2
2019-04-06 14:23:50 +02:00
Jan Tojnar
cb1a20499a
Merge branch 'master' into staging
2019-04-05 11:37:15 +02:00
Bruno Bzeznik
0b03f44c2f
migrate: init at 3.7.2
2019-04-05 09:01:36 +02:00
markuskowa
126e1f8fd0
Merge pull request #58538 from bzizou/stacks
...
stacks: init at 2.3e
2019-04-03 14:41:00 +02:00
Bruno Bzeznik
e7899d2a00
stacks: init at 2.3e
2019-04-03 14:01:32 +02:00
John Ericson
4ccb74011f
Merge commit '18aa59b0f26fc707e7313f8467e67159e61600c2' from master into staging
...
There was one conflict in the NixOS manual; I checked that it still
built after resolving it.
2019-04-01 00:40:03 -04:00
markuskowa
c637aeff19
Merge pull request #58541 from luispedro/add_megahit
...
megahit: init at 1.1.4
2019-03-31 12:51:59 +02:00
Luis Pedro Coelho
bf48451959
megahit: init at 1.1.4
...
This is widely used in bioinformatics for assembling genomes &
metagenomes
2019-03-31 05:56:14 +02:00
R. RyanTM
893abe12e8
bowtie2: 2.3.4.3 -> 2.3.5 ( #58014 )
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/bowtie2/versions
2019-03-31 00:37:38 +01:00
R. RyanTM
2ce544a8b1
minimap2: 2.15 -> 2.16 ( #57319 )
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/minimap2/versions
2019-03-27 23:25:52 +01:00
R. RyanTM
1b73fd1954
paml: 4.9h -> 4.9i ( #57354 )
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/paml/versions
2019-03-27 15:44:21 +01:00
Bruno Bzeznik
00431493c0
itsx: init at 1.1.1
2019-03-26 15:52:35 +01:00
Bruno Bzeznik
6858d0fd62
clustal-omega: init at 1.2.4
2019-03-26 15:45:59 +01:00
Joachim F
c9cd1356ea
Merge pull request #56522 from bzizou/messer-slim
...
messer-slim: init at 3.2.1
2019-03-26 00:42:58 +00:00
Wael M. Nasreddine
5af0780492
Merge remote-tracking branch 'origin/master' into staging
...
* origin/master: (693 commits)
buildGoModule: use go_1_12 instead of go_1_11 (#58103 )
gitAndTools.lab: 0.15.2 -> 0.15.3 (#58091 )
signal-desktop: 1.22.0 -> 1.23.0
added missing semicolon to documentation
terminus_font_ttf: 4.46.0 -> 4.47.0
buildGoModule: remove SSL env vars in favor of cacert in buildInputs (#58071 )
dav1d: init at 0.2.1
dropbox-cli: 2018.11.28 -> 2019.02.14
atlassian-confluence: 6.14.1 -> 6.14.2
maintainers: update email for dywedir
python.pkgs.hglib: use patch to specify hg path (#57926 )
chkrootkit: 0.52 -> 0.53
radare2-cutter: 1.7.2 -> 1.8.0
autorandr: 1.7 -> 1.8
pythonPackages.pyhepmc: fix build
llvm-polly/clang-polly: use latest llvm
apulse: 0.1.11.1 -> 0.1.12, cleanup
factorio: experimental 0.17.14 → 0.17.16 (#58000 )
sequeler: 0.6.7 -> 0.6.8
nasc: 0.5.1 -> 0.5.2
...
2019-03-21 21:01:25 -07:00
Matthew Bauer
37eba81c7b
Merge pull request #56391 from matthewbauer/cmake-treewide
...
Add more CMake flags
2019-03-11 12:43:46 -04:00
Matthew Bauer
6ed49262f5
treewide: remove BUILD_TESTING flag
...
This is now set by CMake
2019-03-11 10:11:28 -04:00
R. RyanTM
70815de29c
picard-tools: 2.18.25 -> 2.18.27
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
2019-03-11 03:37:34 -07:00
R. RyanTM
27e05d81a5
star: 2.7.0a -> 2.7.0c
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/star/versions
2019-03-03 20:55:25 +01:00
R. RyanTM
9989b7c8c4
igv: 2.4.17 -> 2.4.19
...
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/igv/versions
2019-03-03 20:48:52 +01:00