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590 Commits

Author SHA1 Message Date
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
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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) 
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
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 
Semi-automatic update generated by
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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 
Semi-automatic update generated by
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 2018-12-14 16:27:07 -08:00
R. RyanTM
87481c2ff1 star: 2.6.1c -> 2.6.1d 
Semi-automatic update generated by
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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) 
Semi-automatic update generated by
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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 
Semi-automatic update generated by
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 2018-10-24 15:22:22 +02:00
R. RyanTM
269efba0aa bowtie2: 2.3.4.2 -> 2.3.4.3 
Semi-automatic update generated by
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 2018-10-03 21:49:10 -07:00
R. RyanTM
77f8e10fed picard-tools: 2.18.12 -> 2.18.14 (#46978) 
Semi-automatic update generated by
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 2018-09-29 21:03:17 +02:00
Orivej Desh
7545b7dcf3 platypus: 2017-03-07 -> 2018-07-22 2018-09-21 22:42:28 +00:00
Orivej Desh
cefd38b721 samtools: 1.8 -> 1.9 2018-09-21 22:42:28 +00:00
Markus J. Ankenbrand
e2df8e7c0f seaview: init at 4.7 (#46595) 2018-09-13 14:10:44 +02:00
R. RyanTM
c4e8db3de0 star: 2.6.0c -> 2.6.1a (#46176) 
Semi-automatic update generated by
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star
 2018-09-12 22:49:12 +02:00
Matthew Bauer
40d19d8e7c
Merge pull request #45102 from jbedo/hisat2 
hisat2: init 2.1.0
 2018-09-10 15:11:58 -05:00
R. RyanTM
f72cba212c picard-tools: 2.18.11 -> 2.18.12 
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picard-tools
 2018-09-06 14:22:26 -07:00
xeji
6216f5da04
Merge pull request #45263 from r-ryantm/auto-update/bowtie2 
bowtie2: 2.3.4.1 -> 2.3.4.2
 2018-08-21 19:51:36 +02:00
Uli Baum
c47aafde87 bowtie2: broken on aarch64 
never built as far back as hydra logs go.
 2018-08-21 19:11:37 +02:00
Joachim F
6755ab8b34
Merge pull request #44250 from jbedo/strelka 
strelka: init 2.9.5
 2018-08-20 06:24:15 +00:00
Justin Bedo
27960b6acf
strelka: init 2.9.5 2018-08-20 08:58:22 +10:00
Vladimír Čunát
209730208a
Merge branch 'staging-next' 2018-08-17 20:51:31 +02:00
R. RyanTM
73f1448a1f bowtie2: 2.3.4.1 -> 2.3.4.2 
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 2018-08-17 06:50:10 -07:00
Justin Bedo
9bd7a4f520
hisat2: init 2.1.0 2018-08-17 23:03:42 +10:00
Vladimír Čunát
cbabebcc2e
Merge branch 'master' into staging-next 
Hydra: ?compare=1473892
 2018-08-17 13:45:21 +02:00
Jörg Thalheim
0359c5eb65
Merge pull request #45217 from r-ryantm/auto-update/igv 
igv: 2.4.13 -> 2.4.14
 2018-08-17 11:56:26 +01:00
R. RyanTM
33ebfbfcf8 igv: 2.4.13 -> 2.4.14 
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 2018-08-17 01:23:03 -07:00
R. RyanTM
ff7d82d405 picard-tools: 2.18.10 -> 2.18.11 
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 2018-08-16 14:33:38 -07:00
Vladimír Čunát
5b0398dc36
Merge branch 'master' into staging-next 
Conflicts: gobby and libinfinity - I took the hand-edited versions
instead of those resuting from the mass-replacement.

Hydra: ?compare=1473190
 2018-08-13 20:43:59 +02:00
R. RyanTM
f5f55e4727 vcftools: 0.1.15 -> 0.1.16 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/vcftools/versions.
 2018-08-08 00:48:04 -07:00
Tuomas Tynkkynen
008fd5fcf5 Merge remote-tracking branch 'upstream/master' into staging 2018-08-04 15:17:42 +03:00
John Ericson
db965063b3 treewide: Make configureFlags lists 2018-08-03 17:06:03 -04:00
Uli Baum
052e4baf0a somatic-sniper: disable parallel building 
to fix non-deterministic failure
 2018-08-03 08:27:41 +02:00
Justin Bedő
51fc0ef8d2 somatic-sniper: init 1.0.5.0 (#43403) 2018-08-01 22:11:13 +02:00
R. RyanTM
d7c3926352 bcftools: 1.8 -> 1.9 (#43950) 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools. This update was made based on information from https://repology.org/metapackage/bcftools/versions.
 2018-07-30 22:36:27 +02:00
Frederik Rietdijk
5dcb1febac
Merge pull request #43913 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.18.9 -> 2.18.10
 2018-07-22 08:42:32 +02:00
R. RyanTM
668047ca55 picard-tools: 2.18.9 -> 2.18.10 
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.
 2018-07-21 12:28:41 -07:00
volth
52f53c69ce pkgs/*: remove unreferenced function arguments 2018-07-21 02:48:04 +00:00
R. RyanTM
ab535c2757 igv: 2.4.11 -> 2.4.13 
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.
 2018-07-13 02:49:22 -07:00
R. RyanTM
6ec4be7ec5 igv: 2.4.10 -> 2.4.11 (#43003) 
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.

These checks were done:

- built on NixOS
- Warning: no invocation of /nix/store/yc18a4s9rs8m6wjbsmi1lax5v0kkyl2i-igv-2.4.11/bin/igv had a zero exit code or showed the expected version
- 0 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 2.4.11 with grep in /nix/store/yc18a4s9rs8m6wjbsmi1lax5v0kkyl2i-igv-2.4.11
- directory tree listing: https://gist.github.com/ca4cf484aab1c1590806c47c4fdde1d7
- du listing: https://gist.github.com/f7ff80a2429cf0a942195db4944659b1
 2018-07-09 16:02:34 +02:00
Silvan Mosberger
8e2c3b93ba
Merge pull request #43096 from jbedo/mosdepth 
mosdepth: init 0.2.3
 2018-07-09 04:55:24 +02:00
Justin Bedo
59141de608
mosdepth: init 0.2.3 2018-07-09 08:51:49 +10:00
R. RyanTM
cb85999b6b picard-tools: 2.18.7 -> 2.18.9 (#42967) 
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.

These checks were done:

- built on NixOS
- Warning: no invocation of /nix/store/ah3v1x61gmj9lan8a3qvy3824lqvjdgi-picard-tools-2.18.9/bin/picard had a zero exit code or showed the expected version
- 0 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 2.18.9 with grep in /nix/store/ah3v1x61gmj9lan8a3qvy3824lqvjdgi-picard-tools-2.18.9
- directory tree listing: https://gist.github.com/0972acdc51fe8a1cde470e4ab5e87993
- du listing: https://gist.github.com/6a66b6723ce4887cd108678369b87360
 2018-07-06 20:24:57 +02:00
Matthew Bauer
574883f665
Merge pull request #42571 from iimog/hmmer 
hmmer: init at 3.1b2
 2018-06-28 22:00:09 -04:00
Silvan Mosberger
57bccb3cb8 treewide: http -> https sources (#42676) 
* treewide: http -> https sources

This updates the source urls of all top-level packages from http to
https where possible.

* buildtorrent: fix url and tab -> spaces
 2018-06-28 20:43:35 +02:00
Markus Ankenbrand
851ab7f323 hmmer: init at 3.1b2 2018-06-25 16:56:21 +02:00
R. RyanTM
b3052440f6 picard-tools: 2.18.5 -> 2.18.7 (#41975) 
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.

These checks were done:

- built on NixOS
- Warning: no invocation of /nix/store/siklhy9pl9xl9cq3nlqhln038554h72g-picard-tools-2.18.7/bin/picard had a zero exit code or showed the expected version
- 0 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 2.18.7 with grep in /nix/store/siklhy9pl9xl9cq3nlqhln038554h72g-picard-tools-2.18.7
- directory tree listing: https://gist.github.com/a49ed5f2ff312ce6180174183901e38f
- du listing: https://gist.github.com/243f4d89d2100ef27d332e3562d5f173
 2018-06-18 22:41:49 +02:00
R. RyanTM
d97f7d3b89 raxml: 8.2.11 -> 8.2.12 (#41964) 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/RAxML/versions.

These checks were done:

- built on NixOS
- /nix/store/w8iy7fvdwhjw7zx1dkga3v56fz59s7r8-RAxML-8.2.12/bin/raxmlHPC-PTHREADS-SSE3 passed the binary check.
- 1 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 8.2.12 with grep in /nix/store/w8iy7fvdwhjw7zx1dkga3v56fz59s7r8-RAxML-8.2.12
- directory tree listing: https://gist.github.com/8a2b70b299e53bfee9f18d2ab8cd5f9f
- du listing: https://gist.github.com/02803409663f19671adc6be233a327fd
 2018-06-18 22:40:49 +02:00
R. RyanTM
e33eacbc1d picard-tools: 2.18.4 -> 2.18.5 
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.

These checks were done:

- built on NixOS
- Warning: no invocation of /nix/store/y7q0bsph0zldfjkz4ci3f41ba5va810w-picard-tools-2.18.5/bin/picard had a zero exit code or showed the expected version
- 0 of 1 passed binary check by having a zero exit code.
- 0 of 1 passed binary check by having the new version present in output.
- found 2.18.5 with grep in /nix/store/y7q0bsph0zldfjkz4ci3f41ba5va810w-picard-tools-2.18.5
- directory tree listing: https://gist.github.com/1938ad634fa882d94e8d28fd1625547c
- du listing: https://gist.github.com/4b51e89646327900f6ef6f2242f5d0bd
 2018-05-26 10:42:37 -07:00
Arcadio Rubio García
699fa7e953 star: 2.5.3a -> 2.6.0c (#40518) 2018-05-15 15:09:06 +02:00
Arcadio Rubio García
e4a2b70f91 minimap2: init at 2.10 2018-05-14 21:26:07 +01:00
R. RyanTM
47c672b4b1 picard-tools: 2.18.3 -> 2.18.4 
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.

These checks were done:

- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.18.4 with grep in /nix/store/k62ym9i08d0w9sgmdjjfyy4lf2n9ig7p-picard-tools-2.18.4
- directory tree listing: https://gist.github.com/4d9e3062e701681d9b53033dc9511663
 2018-05-12 13:58:09 +02:00
Matthew Justin Bauer
a733bbfb07
Merge pull request #39740 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.18.2 -> 2.18.3
 2018-05-04 17:21:50 -05:00
R. RyanTM
ef01f17c2d paml: 4.9g -> 4.9h 
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.

These checks were done:

- built on NixOS
- ran ‘/nix/store/39cfy96430yznv6h3cg7zd8850i6kdl1-paml-4.9h/bin/chi2 -h’ got 0 exit code
- ran ‘/nix/store/39cfy96430yznv6h3cg7zd8850i6kdl1-paml-4.9h/bin/chi2 --help’ got 0 exit code
- ran ‘/nix/store/39cfy96430yznv6h3cg7zd8850i6kdl1-paml-4.9h/bin/chi2 help’ got 0 exit code
- found 4.9h with grep in /nix/store/39cfy96430yznv6h3cg7zd8850i6kdl1-paml-4.9h
- directory tree listing: https://gist.github.com/b2a37e7cd2b4b41178f0698f3aac69e2
 2018-05-03 15:13:15 +02:00
R. RyanTM
4ea3841d7f picard-tools: 2.18.2 -> 2.18.3 
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.

These checks were done:

- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.18.3 with grep in /nix/store/q67hqz7716nf3c4f8rjmlpf2dqbb06rz-picard-tools-2.18.3
- directory tree listing: https://gist.github.com/6b71ce718f18ef6a48c05457cd0e583b
 2018-04-30 11:43:21 -07:00
Ben Darwin
fa850e8fda conglomerate: init at 2017-09-10 2018-04-27 18:57:17 -04:00
Jörg Thalheim
f7785dd61c
Merge branch 'master' into minc_ecosystem 2018-04-21 20:18:27 +01:00
Jörg Thalheim
39e94277ba
Merge pull request #39197 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.18.1 -> 2.18.2
 2018-04-21 19:21:15 +01:00
R. RyanTM
7d22bbe671 picard-tools: 2.18.1 -> 2.18.2 
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.

These checks were done:

- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.18.2 with grep in /nix/store/sp6gc6c6knpvpsmfdx8074qclcsgs931-picard-tools-2.18.2
- directory tree listing: https://gist.github.com/114857d15222eccda94501b5a871fb24
 2018-04-20 00:44:45 -07:00
R. RyanTM
c478b6217f samtools: 1.7 -> 1.8 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/samtools/versions.

These checks were done:

- built on NixOS
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/samtools --help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/samtools help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/blast2sam.pl -h’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/blast2sam.pl --help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/blast2sam.pl help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/novo2sam.pl help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/psl2sam.pl -h’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/psl2sam.pl --help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/psl2sam.pl help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/soap2sam.pl -h’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/soap2sam.pl --help’ got 0 exit code
- ran ‘/nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8/bin/soap2sam.pl help’ got 0 exit code
- found 1.8 with grep in /nix/store/ip1zr4rg4pwq8f3fs8ar570l0zdicai7-samtools-1.8
- directory tree listing: https://gist.github.com/4673ea3645eb509035dcb386c4ad1da2
 2018-04-10 13:04:09 -07:00
Ben Darwin
de2f36982b ezminc: init at 2017-08-29 2018-04-09 18:07:15 -04:00
Ben Darwin
cf2aac6a04 address license/version issues for PR #29782 2018-04-09 18:06:54 -04:00
Ben Darwin
e90d1e8631 inormalize: init at 1.0.20 (develop branch) 2018-04-09 18:06:54 -04:00
Ben Darwin
54c543b03b n3: init at 1.0.20 2018-04-09 18:06:54 -04:00
Ben Darwin
f532f9f5f4 minc-widgets: init at "1.0.0" (package seems to lack a consistent version) 2018-04-09 18:06:33 -04:00
Ben Darwin
bd460f54a3 mni_autoreg: init at 0.99.70 2018-04-09 18:06:33 -04:00
Ben Darwin
082b3f1058 minc-tools: 2.3.00 -> 2.3.01 (develop branch) 2018-04-09 18:06:33 -04:00
Matthew Justin Bauer
209dce5ada
Merge pull request #38165 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.17.11 -> 2.18.1
 2018-04-08 21:21:14 -05:00
Jörg Thalheim
18fa54032a bcftools: python/perl is needed for shebangs 2018-04-08 09:35:20 +01:00
R. RyanTM
7b75bc79ef bcftools: 1.7 -> 1.8 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/bcftools/versions.

These checks were done:

- built on NixOS
- ran ‘/nix/store/5nqh165r343n7954gm49wbsdwf9iic3l-bcftools-1.8/bin/plot-vcfstats -h’ got 0 exit code
- ran ‘/nix/store/5nqh165r343n7954gm49wbsdwf9iic3l-bcftools-1.8/bin/plot-vcfstats --help’ got 0 exit code
- ran ‘/nix/store/5nqh165r343n7954gm49wbsdwf9iic3l-bcftools-1.8/bin/bcftools -h’ got 0 exit code
- ran ‘/nix/store/5nqh165r343n7954gm49wbsdwf9iic3l-bcftools-1.8/bin/bcftools --help’ got 0 exit code
- ran ‘/nix/store/5nqh165r343n7954gm49wbsdwf9iic3l-bcftools-1.8/bin/bcftools help’ got 0 exit code
- found 1.8 with grep in /nix/store/5nqh165r343n7954gm49wbsdwf9iic3l-bcftools-1.8
- directory tree listing: https://gist.github.com/c9ddd760c0c740dabaabeb604fbb8a5a
 2018-04-07 20:11:48 -07:00
R. RyanTM
34257096e6 igv: 2.4.9 -> 2.4.10 
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.

These checks were done:

- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.4.10 with grep in /nix/store/171fy8d969ynn0m74xi7dxvrbv9di37z-igv-2.4.10
- directory tree listing: https://gist.github.com/9164cca651385e7845f2ac52628d5ad7
 2018-03-31 08:54:46 -07:00
R. RyanTM
d5f23bb90a picard-tools: 2.17.11 -> 2.18.1 
Semi-automatic update generated by https://github.com/ryantm/nixpkgs-update tools.

This update was made based on information from https://repology.org/metapackage/picard-tools/versions.

These checks were done:

- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.18.1 with grep in /nix/store/nxd67d6cdp85kjy0g2qg4005rbwdfj75-picard-tools-2.18.1
- directory tree listing: https://gist.github.com/2fdec4f7617ad9bc0dfcd95a91d4abb6
 2018-03-30 20:27:46 -07:00
Matthew Justin Bauer
964c32bcb3
Merge pull request #36846 from jbedo/snpeff 
snpeff: 4.3t -> 4.3q
 2018-03-19 12:26:33 -05:00
Matthew Justin Bauer
9f58d17d10
Merge pull request #37079 from ryantm/auto-update/picard-tools 
picard-tools: 2.17.10 -> 2.17.11
 2018-03-19 04:04:50 -05:00
Gabriel Ebner
5df4f227ec
Merge pull request #37009 from ryantm/auto-update/igv 
igv: 2.4.8 -> 2.4.9
 2018-03-17 13:43:23 +01:00
Ryan Mulligan
892244dda0 picard-tools: 2.17.10 -> 2.17.11 
Semi-automatic update generated by https://github.com/ryantm/nix-update tools. These checks were done:

- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.17.11 with grep in /nix/store/xmlvcz212yl8bij12jpqibhv8c8mqabs-picard-tools-2.17.11
- found 2.17.11 in filename of file in /nix/store/xmlvcz212yl8bij12jpqibhv8c8mqabs-picard-tools-2.17.11
 2018-03-15 01:16:28 -07:00
Ryan Mulligan
9b4c82d366 igv: 2.4.8 -> 2.4.9 
Semi-automatic update generated by https://github.com/ryantm/nix-update tools. These checks were done:

- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 2.4.9 with grep in /nix/store/q5c9jyg6gc4v3ns7rw5lxj7v4v916a7f-igv-2.4.9
- found 2.4.9 in filename of file in /nix/store/q5c9jyg6gc4v3ns7rw5lxj7v4v916a7f-igv-2.4.9
 2018-03-14 12:04:23 -07:00
Justin Bedo
f48ff649fe
snpeff: 4.3t -> 4.3q 2018-03-12 16:03:44 +11:00
Ryan Mulligan
49272f60dd paml: 4.9c -> 4.9g 
Semi-automatic update. These checks were done:

- built on NixOS
- Warning: no binary found that responded to help or version flags. (This warning appears even if the package isn't expected to have binaries.)
- found 4.9g in filename of file in /nix/store/70p59yxnlzhbj8ig1ax8lrrsdbcf37zp-paml-4.9g
 2018-03-09 07:22:27 -08:00
Ryan Mulligan
0c69b50356 picard-tools: 2.17.4 -> 2.17.10 
Semi-automatic update. These checks were performed:

- built on NixOS
- found 2.17.10 with grep in /nix/store/f74zildbrr99qmp5qkb579x9159n88c6-picard-tools-2.17.10
- found 2.17.10 in filename of file in /nix/store/f74zildbrr99qmp5qkb579x9159n88c6-picard-tools-2.17.10

cc "@jbedo"
 2018-02-28 15:02:46 +00:00
Ryan Mulligan
d1dc4cae54 igv: 2.4.6 -> 2.4.8 
Semi-automatic update. These checks were performed:

- built on NixOS
- found 2.4.8 with grep in /nix/store/3vwg5hpprkm3v345fy05gxdjicfakql7-igv-2.4.8
- found 2.4.8 in filename of file in /nix/store/3vwg5hpprkm3v345fy05gxdjicfakql7-igv-2.4.8

cc "@mimadrid"
 2018-02-26 19:11:52 -08:00
adisbladis
e046d8bc08
Merge pull request #35555 from ryantm/auto-update/bcftools-1.6-to-1.7 
bcftools: 1.6 -> 1.7
 2018-02-26 17:39:46 +08:00
Ryan Mulligan
bc730862d5 bowtie2: 2.3.4 -> 2.3.4.1 
Semi-automatic update. These checks were performed:

- built on NixOS
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-s -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-s --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-s --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-s -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-s --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-l -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-l --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-l --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-l -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build-l --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-s -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-s --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-s --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-s -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-s --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-l -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-l --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-l --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-l -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-align-l --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-s -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-s --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-s --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-s -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-s --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-l -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-l --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-l --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-l -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect-l --help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect -V` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect -v` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-inspect help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build -V` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build -v` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2-build help` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2 -h` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2 --help` got 0 exit code
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2 --version` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2 -h` and found version 2.3.4.1
- ran `/nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1/bin/bowtie2 --help` and found version 2.3.4.1
- found 2.3.4.1 with grep in /nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1
- found 2.3.4.1 in filename of file in /nix/store/3dhsbc2qzhls7p7xl8x5jzjk51l6y891-bowtie2-2.3.4.1
 2018-02-25 09:45:04 -08:00
Ryan Mulligan
9af7602b8a bcftools: 1.6 -> 1.7 
Semi-automatic update. These checks were performed:

- built on NixOS
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools -h` got 0 exit code
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools --help` got 0 exit code
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools help` got 0 exit code
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools -v` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools --version` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools version` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools -h` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools --help` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/bcftools help` and found version 1.7
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/plot-vcfstats -h` got 0 exit code
- ran `/nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7/bin/plot-vcfstats --help` got 0 exit code
- found 1.7 with grep in /nix/store/5yasri83ahcvhx06dv92fpzmxay9c833-bcftools-1.7
 2018-02-25 09:02:06 -08:00
Jörg Thalheim
08d1400816
Merge pull request #34530 from unode/samtools-old 
samtools-old: init at 0.1.19
 2018-02-10 08:34:26 +00:00
Jörg Thalheim
80b096b2b3
Merge pull request #34531 from unode/raxml 
RAxML: init at 8.2.11 (SSE3 & MPI)
 2018-02-10 08:32:19 +00:00
Renato Alves
154d1d2f19
samtools: 1.6 -> 1.7 2018-02-06 15:38:00 +01:00
Renato Alves
65ea5f8857
samtools_0_1_19: init at 0.1.19 
samtools-1.5 already exists but some software requires the older version
 2018-02-02 21:49:50 +01:00
Renato Alves
05889c52b9
RAxML: init at 8.2.11 (SSE3 & MPI) 
This can potentially be extended to cover all the other compilation
targets. SSE3-PTHREADS and MPI being the most commonly used.
 2018-02-02 18:31:40 +01:00
Renato Alves
b22e4976cb
muscle: init at 3.8.31 2018-01-28 12:32:46 +01:00
Alexey Shmalko
38fbc93f46
Merge pull request #34156 from arcadio/star 
star: init at 2.5.3a
 2018-01-27 17:02:16 +02:00
adisbladis
7a2d35d9db
Merge pull request #34119 from arcadio/master 
igv: 2.3.98 -> 2.4.6
 2018-01-25 18:33:49 +08:00
Samuel Leathers
efdb0983da
Merge pull request #34199 from arcadio/kallisto 
kallisto: init at 0.43.1
 2018-01-24 20:43:24 -07:00
Arcadio Rubio García
a7333e9ced kallisto: init at 0.43.1 2018-01-24 16:16:46 +00:00
Arcadio Rubio García
72d675b23c star: init at 2.5.3a 2018-01-24 16:07:15 +00:00
adisbladis
266979a360
Merge pull request #34125 from arcadio/bwa 
bwa: 0.7.16a -> 0.7.17
 2018-01-23 20:12:56 +08:00
adisbladis
b0603f514b
Merge pull request #34139 from arcadio/bedtools 
bedtools: 2.26.0 -> 2.27.1
 2018-01-23 12:56:01 +08:00
adisbladis
7490d4d698
Merge pull request #34140 from arcadio/picard 
picard-tools: 2.7.1 -> 2.17.4
 2018-01-22 23:57:10 +08:00
Arcadio Rubio García
612953567d bowtie2: 2.3.3.1 -> 2.3.4 2018-01-22 12:28:06 +00:00
Arcadio Rubio García
12c5dc343f picard-tools: 2.7.1 -> 2.17.4 2018-01-22 12:16:26 +00:00
Arcadio Rubio García
c75e91a374 bedtools: 2.26.0 -> 2.27.1 2018-01-22 12:09:44 +00:00
Arcadio Rubio García
0d05bcae8c bwa: 0.7.16a -> 0.7.17 2018-01-22 01:58:36 +00:00
Arcadio Rubio García
550e6146d4 igv: 2.3.98 -> 2.4.6 2018-01-21 21:07:44 +00:00
Ashley Gillman
245a67df8b dcm2niix: cmake is native, style 2018-01-15 16:53:28 +10:00
Ashley Gillman
271d4a7ca0 dcm2niix: init at 1.0.20170130 2018-01-15 16:45:03 +10:00
Justin Bedo
a49c91f655
snpeff: 4.3p -> 4.3t 2017-12-21 10:52:26 +11:00
Orivej Desh
1f99fd6965 libminc: fix build after hdf5 upgrade by using hdf5_1_8 2017-12-01 00:37:29 +00:00
rybern
ef0486b1f9 vcftools: init at 0.1.15 (#31339) 2017-11-16 09:52:56 +02:00
Ryan Bernstein
941014ffff bowtie2: init at 2.3.3.1 2017-10-22 00:11:49 +02:00
Orivej Desh
047c576353 Merge pull request #29963 from mimadrid/update/samtools-1.6.0 
samtools: 1.5.0 -> 1.6.0
 2017-10-02 01:07:11 +00:00
Orivej Desh
d73bd7f50a bcftools: fix up 2017-10-01 07:45:19 +00:00
Orivej Desh
09a5396982 samtools: fix up 2017-10-01 07:36:30 +00:00
mimadrid
bebccf176e
bcftools: 1.5.0 -> 1.6.0 2017-09-30 22:22:25 +02:00
mimadrid
ee2c76693e
samtools: 1.5.0 -> 1.6.0 2017-09-30 22:20:02 +02:00
Robin Gloster
7cbf3a27de freebayes: clean up build 2017-09-28 00:54:01 +02:00
Samuel Leathers
a3e2ecd7f7 freebayes: 1.1.0 -> 2017-08-23 2017-09-28 00:54:01 +02:00
Tuomas Tynkkynen
4b4bfbf3e5 darwin: Disable another bunch of packages never having built successfully 
tecoc: https://hydra.nixos.org/build/61141995
shallot: https://hydra.nixos.org/build/61145497
plink-ng: https://hydra.nixos.org/build/61130149
tshark: https://hydra.nixos.org/build/61479600
 2017-09-22 19:49:57 +03:00
Ben Darwin
c7bbe471b0 ants: bump version and fix sandboxed build 2017-09-20 18:42:34 -04:00
Robin Gloster
a0967948d9
bwa: 0.7.15 -> 0.7.16a 2017-09-05 14:42:45 +02:00
Samuel Leathers
d9cd226a6d neuron: 7.4 -> 7.5 2017-09-02 16:58:14 -04:00
Ryan Bernstein
749e702a46 poretools: version number to commit date 2017-08-18 09:59:26 -04:00
Ryan Bernstein
a13e4ad1f5 poretools: init at 0.6.0 2017-08-17 11:17:30 -04:00
mimadrid
15a99ae367
bcftools: 1.4.0 -> 1.5.0 2017-08-13 00:17:48 +02:00
mimadrid
ca45a26ec3
samtools: 1.4.0 -> 1.5.0 2017-08-13 00:17:25 +02:00
Silvan Mosberger
f5fa5fa4d6 pkgs: refactor needless quoting of homepage meta attribute (#27809) 
* pkgs: refactor needless quoting of homepage meta attribute

A lot of packages are needlessly quoting the homepage meta attribute
(about 1400, 22%), this commit refactors all of those instances.

* pkgs: Fixing some links that were wrongfully unquoted in the previous
commit

* Fixed some instances
 2017-08-01 22:03:30 +02:00
mimadrid
20fb18bdbc
igv: 2.3.89 -> 2.3.98 2017-08-01 20:46:31 +02:00
Shea Levy
24c59a4452 neuron: enable GUI 2017-06-28 11:59:54 -04:00
Justin Bedo
94ec54598c
snpeff: 4.3i -> 4.3p 2017-06-13 15:31:52 +10:00
Jörg Thalheim
be19ad150c Merge pull request #25594 from mimadrid/update/htslib-1.4 
Update/htslib 1.4
 2017-05-11 07:08:56 +01:00
mimadrid
8d1bebf83c
bcftools: 1.3.1 -> 1.4 2017-05-11 07:04:33 +01:00
mimadrid
9073e67568
samtools: 1.3.1 -> 1.4 2017-05-07 23:15:48 +02:00
Aneesh Agrawal
bd9246b009 treewide: Always use integers for meta.priority 
Meta attributes types are now enforce as of commit
90b9719f4f,
so ensure meta.priority is always set to an integer.

This fixes evaluation of `linuxPackages_latest.virtualbox`
(the impetus for this commit)
and other packages that use lowPrio or hiPrio.
 2017-05-02 01:43:22 -04:00
Michael Raskin
7ef99bf054 Merge pull request #24085 from bcdarwin/ants 
ants: set $ANTSPATH variable in shell scripts
 2017-04-30 23:03:06 +02:00
Matthias Beyer
6239da6ade diamond: init at 0.8.36 2017-04-12 13:05:57 +02:00
Justin Bedő
c5015b77af platypus: fix platforms metadata (#24666) 2017-04-06 10:10:54 +01:00
Robin Gloster
b9948fedc6
ncbi_tools: mark as broken and remove -fPIC 
PIC is used by default since 16.09
 2017-03-30 16:23:34 +02:00
Ben Darwin
fbc9a4d7dc ants: set $ANTSPATH variable in shell scripts 2017-03-22 16:01:05 -04:00
Franz Pletz
bfb7890fa0 Merge pull request #24191 from jbedo/bedtools 
bedtools: fix clang build
 2017-03-22 15:30:19 +01:00
Justin Bedo
56aeb271c9
bedtools: fix clang build 2017-03-22 12:00:24 +11:00
Dan Peebles
7ad3fd7ca7 neuron: fix on clang 3.8 and above 
This is in preparation for upgrading Darwin stdenv to LLVM 4
 2017-03-21 01:00:18 -04:00
Michael Raskin
4d5f33deff Merge pull request #23376 from bcdarwin/ants 
ANTs: init at 2.1.0 (0gyys1lf) and update ITK accordingly
 2017-03-18 18:42:24 +01:00
Robin Gloster
e2a13af49c
emboss: fix build 2017-03-13 13:15:51 +01:00
Justin Bedo
1ac797861b
SnpEff: init at 4.3i 2017-03-08 22:43:50 +01:00
Justin Bedo
076e513b94
varscan: init at 2.4.2 2017-03-08 22:43:49 +01:00
Justin Bedo
4bb50fd08c
picard-tools: init at 2.7.1 2017-03-08 22:43:45 +01:00
Justin Bedo
7f214e6410
bedtools: init at 2.26.0 2017-03-08 22:36:29 +01:00
Justin Bedo
661048c803
platypus: init at 2017-03-07 2017-03-08 22:36:03 +01:00
Ben Darwin
05359c327b ANTs: init at 2.1.0 (0gyys1lf) 2017-03-01 21:06:30 -05:00
Celine Mercier
78c052e91a
ecopcr: init at 0.8.0 2017-02-06 16:01:08 +01:00
Ian Lancaster
5f67b7b30a emboss: 6.0.1 -> 6.6.0 2017-02-04 19:05:48 -05:00
mimadrid
29cb10c021
igv: 2.3.77 -> 2.3.89 2016-12-23 19:37:10 -05:00
Jason Daniel Augustine Gilliland
59ca5d213f freebayes: init at 1.1.0 
Signed-off-by: zimbatm <zimbatm@zimbatm.com>
 2016-12-22 14:10:37 +00:00
Justin Bedo
a6d6a3972f
plink-ng: init at 1.90b3 2016-11-14 20:28:39 +11:00
Justin Bedo
ec31e2cc27
Fix bcftools installation prefix 2016-11-09 08:03:04 +11:00
Tim Steinbach
6d11e8ed4c
Remove pal2nal 
No longer build/exists
 2016-11-03 21:58:47 -04:00
Tim Steinbach
c36a1d6502
paml: 4.2a -> 4.9c 2016-11-03 21:33:19 -04:00
obadz
2919375c91 minc_tools: don't run tests which have been failing since first pkged 2016-09-05 17:26:12 +01:00
Adrien Devresse
28d2d78b55 neuron: fix issue with incorrectly prefixed python path 2016-09-01 13:41:26 +02:00
Frederik Rietdijk
684f08166c fixup 2016-09-01 12:03:10 +02:00
Adrien Devresse
ae2800378f neuron: fix issue #17914 -> Add python bindings to neuron derivation and minor fixes 
- Add support for python bindings
- make neuron respect standard pythonpath prefix
- force exec_prefix == prefix to respect standard nix file hierarchy
- normalize indentation
- propagate dependencies necessary for nrniv_makefile usage
- Add support for darwin
 2016-09-01 12:03:10 +02:00
Matthew Bauer
96322f6926 bcftools: fix darwin building 
gcc not available
 2016-08-10 22:48:19 -05:00
Tuomas Tynkkynen
f87f37c1ee bwa: Broken on i686 
http://hydra.nixos.org/build/38236956
 2016-08-06 17:06:45 +03:00
Tuomas Tynkkynen
21f17d69f6 treewide: Add lots of meta.platforms 
Build-tested on x86_64 Linux & Mac.
 2016-08-02 21:42:43 +03:00
Tuomas Tynkkynen
102ffa6be7 treewide: Wrap some really long package descriptions 2016-08-02 21:17:44 +03:00
mimadrid
5c7a75412e
igv: init at 2.3.77 2016-06-26 19:27:56 +02:00
Joachim Fasting
46b07b335b Merge pull request #16379 from mimadrid/init/bcftools-1.3.1 
bcftools: init at 1.3.1
 2016-06-24 22:15:51 +02:00
mimadrid
d91d245f16
bcftools: init at 1.3.1 2016-06-24 21:08:17 +02:00
mimadrid
14feec44e4
samtools: refactoring 2016-06-24 21:08:17 +02:00
Luis Pedro Coelho
bd617cb185 init bwa at 0.7.15 
Closes #16064
 2016-06-08 17:25:20 +01:00
Tobias Geerinckx-Rice
dce1edf946
samtools: 1.3 -> 1.3.1 2016-05-25 02:06:47 +02:00
Louis Taylor
70c1b2b1c0 samtools: init at 1.3 2016-04-12 20:13:40 +01:00
Ben Darwin
69c628e1ff minc-tools: init at 2.3.00 2016-02-23 14:03:56 -05:00
devresse
4046d3ce8d neuron: init at 7.4 2016-02-21 15:02:47 +00:00
Tobias Geerinckx-Rice
7b6d9d4cff Remove arb and then-orphaned lesstif93 
Arb has been broken (and marked as such) since the removal of
GCC 4.2 in July 2014. Nothing and no-one uses it. Time to go.
 2015-05-26 11:46:41 +02:00
Bjørn Forsman
c9baba9212 Fix many package descriptions 
(My OCD kicked in today...)

Remove repeated package names, capitalize first word, remove trailing
periods and move overlong descriptions to longDescription.

I also simplified some descriptions as well, when they were particularly
long or technical, often based on Arch Linux' package descriptions.

I've tried to stay away from generated expressions (and I think I
succeeded).

Some specifics worth mentioning:
 * cron, has "Vixie Cron" in its description. The "Vixie" part is not
   mentioned anywhere else. I kept it in a parenthesis at the end of the
   description.

 * ctags description started with "Exuberant Ctags ...", and the
   "exuberant" part is not mentioned elsewhere. Kept it in a parenthesis
   at the end of description.

 * nix has the description "The Nix Deployment System". Since that
   doesn't really say much what it is/does (especially after removing
   the package name!), I changed that to "Powerful package manager that
   makes package management reliable and reproducible" (borrowed from
   nixos.org).

 * Tons of "GNU Foo, Foo is a [the important bits]" descriptions
   is changed to just [the important bits]. If the package name doesn't
   contain GNU I don't think it's needed to say it in the description
   either.
 2014-08-24 22:31:37 +02:00
Eelco Dolstra
8a7f3c3618 Mark a bunch of packages as broken or not supported on Darwin 2014-08-08 17:59:02 +02:00
Mateusz Kowalczyk
7a45996233 Turn some license strings into lib.licenses values 2014-07-28 11:31:14 +02:00
Eelco Dolstra
6f11a6681d arb: Mark as broken 2014-07-22 15:12:21 +02:00
Bjørn Forsman
28ac782583 Some description fixes 
There are many more packages to fix, this is just a start.

Rules:
 * Don't repeat the package name (not always that easy...)
 * Start with capital letter
 * Don't end with full stop
 * Don't start with "The ..." or "A ..."

I've also added descriptions to some packages and rewritten others.
 2013-10-05 19:36:23 +02:00
Justin Bedo
c38ffa7b7d Added expression for PLINK 2013-09-19 09:39:14 +10:00
Eelco Dolstra
5553546c21 Remove a bunch of unreferenced files 
Plus a small number of obsolete packages (like old versions of qemu).
 2012-11-29 13:43:37 +01:00
Yury G. Kudryashov
75207a6a90 Try to update slr 
Still fails to build because atlas doesn't provide full blas.

svn path=/nixpkgs/trunk/; revision=33164
 2012-03-16 17:15:52 +00:00
Eelco Dolstra
c556a6ea46 * "ensureDir" -> "mkdir -p". "ensureDir" is a rather pointless 
function, so obsolete it.

svn path=/nixpkgs/branches/stdenv-updates/; revision=31644
 2012-01-18 20:16:00 +00:00
Eelco Dolstra
f1598a8941 * More cleanup. 
svn path=/nixpkgs/trunk/; revision=22798
 2010-07-28 18:01:17 +00:00
Pjotr Prins
17e2100b03 Updated PAML package to 4.2a 
svn path=/nixpkgs/trunk/; revision=14262
 2009-02-26 15:22:13 +00:00
Pjotr Prins
7ba68d934f Added note on package status for 64 bits 
svn path=/nixpkgs/trunk/; revision=14090
 2009-02-17 08:23:21 +00:00
Pjotr Prins
387a7a85d6 Updated NCBI tools to latest version 
svn path=/nixpkgs/trunk/; revision=14087
 2009-02-16 16:38:55 +00:00
Pjotr Prins
3ce5cba9c7 Added pkgMaintainer info to these 'biology' section packages. 
svn path=/nixpkgs/trunk/; revision=12987
 2008-10-07 15:12:06 +00:00
Pjotr Prins
b3aa5d6bfc Added meta.pkgMaintainer to biology packages - a claim to fame, or 
you know who to blame!

svn path=/nixpkgs/trunk/; revision=12986
 2008-10-07 15:12:01 +00:00
Pjotr Prins
4ab58fc7f3 Squashed commit of the following: 
commit 74c0e9192e17d9dfce50f811fdb7e82a2785134e
Author: Pjotr <pjotr.public05@thebird.nl>
Date:   Tue Oct 7 16:33:39 2008 +0200

    Merge

commit ad91fb07a47226ed9e99f2dcb55b69ea0e70aa84
Author: Pjotr <pjotr.public05@thebird.nl>
Date:   Tue Oct 7 16:23:20 2008 +0200

    openmotif: added some comments on license and download

commit 68a552975f5c7e0964c7c9625e08de0864757255
Author: Pjotr <pjotr.public05@thebird.nl>
Date:   Tue Oct 7 16:10:49 2008 +0200

    Match parameters so arb starts compiling against openmotif

commit 16c52fb4071193f89acf6f7f53cfeff322285555
Author: Pjotr <pjotr.public05@thebird.nl>
Date:   Tue Oct 7 16:04:06 2008 +0200

    Added openmotif package

commit 75c4bba418f16859e99e97f48785e27ad87e99f5
Author: Pjotr <pjotr.public05@thebird.nl>
Date:   Tue Oct 7 15:20:55 2008 +0200

    Adding openmotif

commit 83a847d194b007e2ef856f2a5ad7c49939b6cf8c
Merge: 52918f1... 5ba4f06...
Author: Pjotr <pjotr.public05@thebird.nl>
Date:   Tue Oct 7 14:15:05 2008 +0200

    Merge branch 'syncsvn'

    Conflicts:
    	pkgs/top-level/all-packages.nix

commit 52918f1f3af55429cc80c99d695e4a8d8b7869b0
Author: Pjotr Prins <wrk@nema-ws01.wurnet.nl>
Date:   Mon Oct 6 18:31:06 2008 +0200

    arb: Removed xfig as dependency (will add later)
    arb: Don't recurse chmod settings of shared dir

commit c283733782dcbf0dcd88710e83f3eededf8f0866
Merge: e434cdf... a51773a...
Author: Pjotr Prins <wrk@nema-ws01.wurnet.nl>
Date:   Mon Oct 6 17:09:42 2008 +0200

    Merge branch 'master' of ssh://bio4.xparrot.eu//export/data/repositories/git/nixpkgs-testing-pjotr

commit a51773a3d4295d7ce16e6a7e983ded814180e30a
Merge: 290ae0b... 241012c...
Author: Pjotr <pjotr.public05@thebird.nl>
Date:   Mon Oct 6 16:54:14 2008 +0200

    Merge branch 'master' of ssh://bio4.xparrot.eu//export/data/repositories/git/nixpkgs-testing-pjotr

commit e434cdf9b9acefab4f54e18204ff16af179c442d
Merge: ef57566... 241012c...
Author: Pjotr Prins <wrk@nema-ws01.wurnet.nl>
Date:   Mon Oct 6 16:12:27 2008 +0200

    Merge branch 'master' of ssh://bio4.xparrot.eu//export/data/repositories/git/nixpkgs-testing-pjotr

commit 241012cae194d0f770be2224b5bb18b66e3ae0f0
Author: Pj <wrk@bio03.(none)>
Date:   Mon Oct 6 16:11:11 2008 +0200

    Added older version of lesstif for arb

commit 290ae0b802285a8dda41b3c5730e53239d73b47c
Merge: dfdf7fe... 53b6ceb...
Author: Pjotr <pjotr.public05@thebird.nl>
Date:   Mon Oct 6 15:20:17 2008 +0200

    Merge branch 'master' of ssh://bio4.xparrot.eu//export/data/repositories/git/nixpkgs-testing-pjotr

commit dfdf7fe8ac9599ec372bdb83630a236f227ad7d5
Author: Pjotr <pjotr.public05@thebird.nl>
Date:   Mon Oct 6 15:15:04 2008 +0200

    Fixed missing parameters for arb - and added kernelHeaders_2.6.18

commit ef57566834eb786cdcb57a799b7d1cb284eee389
Author: Pjotr Prins <wrk@nema-ws01.wurnet.nl>
Date:   Mon Oct 6 15:06:26 2008 +0200

    Changed arb permissions and priority

svn path=/nixpkgs/trunk/; revision=12985
 2008-10-07 14:35:11 +00:00
Pjotr Prins
bd0b84b3c7 Changed arb permissions and priority 
svn path=/nixpkgs/trunk/; revision=12969
 2008-10-06 13:17:56 +00:00
Pjotr Prins
6d70506401 Small fixes to ARB 
Included older kernel headers

svn path=/nixpkgs/trunk/; revision=12961
 2008-10-05 10:56:47 +00:00
Pjotr Prins
c38a72a573 Added more dependencies for ARB 
svn path=/nixpkgs/trunk/; revision=12959
 2008-10-05 10:56:44 +00:00
Pjotr Prins
fcb2efbc92 Added shared dir and updated reference to ARB 
svn path=/nixpkgs/trunk/; revision=12958
 2008-10-05 10:56:23 +00:00
Pjotr Prins
29d6189e8b The arb package (biology) 
svn path=/nixpkgs/trunk/; revision=12956
 2008-10-05 09:03:58 +00:00
Pjotr Prins
034f28e268 Biology package 
svn path=/nixpkgs/trunk/; revision=12953
 2008-10-05 09:00:19 +00:00
Pjotr Prins
df1e47822b Lower priority of this package because of zlib.so conflict 
svn path=/nixpkgs/trunk/; revision=12945
 2008-10-05 08:42:40 +00:00
Pjotr Prins
c09e1e540c Introduced pal2nal package 
svn path=/nixpkgs/trunk/; revision=12896
 2008-09-19 13:39:17 +00:00
Pjotr Prins
301f2e3094 Bumped PAML version 
svn path=/nixpkgs/trunk/; revision=12895
 2008-09-19 13:36:35 +00:00
Pjotr Prins
2a845ebb7a Removing clustalw2 package - may come back later 
svn path=/nixpkgs/trunk/; revision=12400
 2008-07-23 08:37:00 +00:00
Pjotr Prins
0014ffcbae Updated emboss package to 6.0.1 
svn path=/nixpkgs/trunk/; revision=12399
 2008-07-23 08:22:23 +00:00
Pjotr Prins
0e751ebadc Long description 
svn path=/nixpkgs/trunk/; revision=12005
 2008-06-07 06:41:18 +00:00
Pjotr Prins
289da88ccc Moved NCBI-tools to applications 
svn path=/nixpkgs/trunk/; revision=12004
 2008-06-07 06:34:02 +00:00
Pjotr Prins
f9e018c80d biology/paml added 
svn path=/nixpkgs/trunk/; revision=11997
 2008-06-06 08:23:49 +00:00
Pjotr Prins
62c9176206 Added emboss 
svn path=/nixpkgs/trunk/; revision=11993
 2008-06-05 17:14:33 +00:00
Pjotr Prins
5866a8b101 tabs2spaces of .nix file 
svn path=/nixpkgs/trunk/; revision=11992
 2008-06-05 16:58:41 +00:00
Pjotr Prins
13463a6f01 MrBayes - a biology package for phylogeny 
svn path=/nixpkgs/trunk/; revision=11986
 2008-06-05 13:35:45 +00:00
Pjotr Prins
849e3eb21c biology/clustalw2 package 
svn path=/nixpkgs/trunk/; revision=11631
 2008-04-15 09:32:12 +00:00