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347 commits

Author SHA1 Message Date
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 
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

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* 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 
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 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 
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 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 
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 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 
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 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 
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 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) 
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 2019-04-20 13:15:40 +02:00
Aaron Andersen
11cf1a282d
Merge pull request #58377 from bzizou/exonerate 
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 
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 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) 
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 2019-03-31 00:37:38 +01:00
R. RyanTM
2ce544a8b1 minimap2: 2.15 -> 2.16 (#57319) 
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 2019-03-27 23:25:52 +01:00
R. RyanTM
1b73fd1954 paml: 4.9h -> 4.9i (#57354) 
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 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 
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 2019-03-11 03:37:34 -07:00
R. RyanTM
27e05d81a5 star: 2.7.0a -> 2.7.0c 
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 2019-03-03 20:55:25 +01:00
R. RyanTM
9989b7c8c4 igv: 2.4.17 -> 2.4.19 
Semi-automatic update generated by
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 2019-03-03 20:48:52 +01:00
Bruno Bzeznik
598f11862c messer-slim: init at 3.2.1 2019-02-28 15:11:18 +01:00
tbenst
1cb81a69a0 cmtk: init at 3.3.1 (#54016) 
* cmtk: init at 3.3.1
 2019-02-08 17:41:14 -05:00
markuskowa
0496c08afd
Merge pull request #55298 from r-ryantm/auto-update/igv 
igv: 2.4.16 -> 2.4.17
 2019-02-06 12:50:24 +01:00
R. RyanTM
da628f0cbd igv: 2.4.16 -> 2.4.17 
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 2019-02-05 20:06:55 -08:00
R. RyanTM
e27eaf6111 star: 2.6.1d -> 2.7.0a 
Semi-automatic update generated by
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 2019-02-03 17:20:27 -08:00
markuskowa
e27e114803
Merge pull request #53677 from jbedo/snpeff-4.3T 
snpeff: 4.3q -> 4.3t
 2019-01-31 10:36:32 +01:00
Justin Bedo
75dd587793
snpeff: 4.3q -> 4.3t 2019-01-31 15:15:05 +11:00
R. RyanTM
2b39f17d08 minimap2: 2.14 -> 2.15 
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 2019-01-28 20:01:47 +00:00
R. RyanTM
00cdff318a picard-tools: 2.18.23 -> 2.18.25 
Semi-automatic update generated by
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 2019-01-28 17:17:30 +00:00
R. RyanTM
b2a7ef628a picard-tools: 2.18.21 -> 2.18.23 
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 2019-01-16 21:43:19 -08:00
R. RyanTM
26b492b207 minimap2: 2.10 -> 2.14 (#52845) 
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 2019-01-13 22:34:45 +01:00
tbenst
d34f2b9b96 bftools: init at 5.9.2 (#53769) 2019-01-10 18:28:28 -05:00
Frederik Rietdijk
2da31b80bb Merge master into staging-next 2019-01-03 20:07:35 +01:00
R. RyanTM
c00dbcb7c4 picard-tools: 2.18.20 -> 2.18.21 
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 2019-01-03 08:39:10 +01:00
Frederik Rietdijk
10afccf145 Merge staging-next into staging 2018-12-27 18:11:34 +01:00
R. RyanTM
338cf1a7fc igv: 2.4.15 -> 2.4.16 
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 2018-12-26 10:44:01 +01:00
Jan Tojnar
ef935fa101
Merge branch 'master' into staging 2018-12-24 15:02:29 +01:00
Renaud
6f5ec9d889
Merge pull request #52134 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.18.17 -> 2.18.20
 2018-12-19 17:53:47 +01:00
Frederik Rietdijk
9ab61ab8e2 Merge staging-next into staging 2018-12-19 09:00:36 +01:00
volth
fed7914539
Merge branch 'staging' into make-perl-pathd 2018-12-18 17:13:27 +00:00
markuskowa
96b0a38f07
Merge pull request #52015 from r-ryantm/auto-update/star 
star: 2.6.1c -> 2.6.1d
 2018-12-16 23:38:37 +01:00
volth
bb9557eb7c lib.makePerlPath -> perlPackages.makePerlPath 2018-12-15 03:50:31 +00:00
R. RyanTM
b261fb0474 picard-tools: 2.18.17 -> 2.18.20 
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 2018-12-14 16:27:07 -08:00
R. RyanTM
87481c2ff1 star: 2.6.1c -> 2.6.1d 
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 2018-12-14 01:07:34 -08:00
Maximilian Bosch
de02111a51
Merge pull request #51534 from jbedo/bowtie2 
bowtie2: fix missing dependencies
 2018-12-10 00:58:51 +01:00
Justin Bedo
8c5251e3c0
bowtie2: fix missing dependencies 2018-12-05 10:51:30 +11:00
Frederik Rietdijk
9b81c7e455 Merge staging-next into staging 2018-11-29 09:18:35 +01:00
R. RyanTM
36a0335d02 picard-tools: 2.18.14 -> 2.18.17 (#50647) 
* picard-tools: 2.18.14 -> 2.18.16

Changelog: https://github.com/broadinstitute/picard/releases/tag/2.18.16
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* picard-tools: 2.18.16 -> 2.18.17

Changelog: https://github.com/broadinstitute/picard/releases/tag/2.18.17
 2018-11-27 14:31:09 +01:00
Matthew Bauer
d492f53faf
Merge pull request #50527 from matthewbauer/ninja-check-phase 
Add check phase to ninja setup hook
 2018-11-20 16:55:12 -06:00
Matthew Bauer
2c47a4229f treewide: remove ctest usages 
These are already in the generated makefiles!
 2018-11-18 19:31:02 -06:00
Ben Darwin
cb6d819b93 niftyseg: init at 1.0.0 2018-11-16 12:29:29 -05:00
Ben Darwin
6aa3deeb50 niftyreg: init at 1.3.9 2018-11-16 12:24:53 -05:00
Markus J. Ankenbrand
bf05da0967 hmmer: 3.1b2 -> 3.2.1 (#50284) 
This version was released in June 2018 and has many bug fixes
and improvements compared to the previous version from 2015.
See: https://cryptogenomicon.org/2018/06/07/hmmer-3-2-release/
 2018-11-13 15:43:44 +01:00
R. RyanTM
37f01d5bf8 igv: 2.4.14 -> 2.4.15 (#50087) 
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 2018-11-09 22:42:04 -05:00
royneary
bb2bae6986 mosdeph: fix compilation with nim 0.19 2018-10-31 22:03:27 +01:00
R. RyanTM
c759273e2e star: 2.6.1a -> 2.6.1c 
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 2018-10-24 15:22:22 +02:00
R. RyanTM
269efba0aa bowtie2: 2.3.4.2 -> 2.3.4.3 
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 2018-10-03 21:49:10 -07:00
R. RyanTM
77f8e10fed picard-tools: 2.18.12 -> 2.18.14 (#46978) 
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 2018-09-29 21:03:17 +02:00