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283 commits

Author SHA1 Message Date
R. RyanTM 8ebf0eefbe star: 2.7.0f -> 2.7.1a (#62577) 
* star: 2.7.0f -> 2.7.1a

Semi-automatic update generated by
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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 
Semi-automatic update generated by
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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 
Semi-automatic update generated by
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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 
Semi-automatic update generated by
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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 
Semi-automatic update generated by
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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 
Semi-automatic update generated by
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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) 
Semi-automatic update generated by
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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 
Semi-automatic update generated by
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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) 
Semi-automatic update generated by
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 2019-03-31 00:37:38 +01:00
R. RyanTM 2ce544a8b1 minimap2: 2.15 -> 2.16 (#57319) 
Semi-automatic update generated by
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 2019-03-27 23:25:52 +01:00
R. RyanTM 1b73fd1954 paml: 4.9h -> 4.9i (#57354) 
Semi-automatic update generated by
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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 
Semi-automatic update generated by
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 2019-03-11 03:37:34 -07:00
R. RyanTM 27e05d81a5 star: 2.7.0a -> 2.7.0c 
Semi-automatic update generated by
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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