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299 commits

Author SHA1 Message Date
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
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 
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 
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
volth f3282c8d1e treewide: remove unused variables (#63177) 
* treewide: remove unused variables

* making ofborg happy
 2019-06-16 19:59:05 +00:00
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
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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
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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 
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