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527 Commits

Author SHA1 Message Date
Bruno Bzeznik
f7a4e4a93a bayescan: init at 2.1 (#68191) 
Co-authored-by: Dmitry Kalinkin <dmitry.kalinkin@gmail.com>
 2020-01-09 12:38:53 -05:00
Luis Pedro Coelho
fdfebafc10 blast: init at 2.10.0 (#61430) 
Co-authored-by: Pavel Chuprikov <pschuprikov@gmail.com>
 2020-01-07 20:14:18 +01:00
R. RyanTM
4bc4c70bc6 last: 1042 -> 1045 2020-01-06 11:46:28 -08:00
Frederik Rietdijk
7aa2b0215b Merge master into staging-next 2020-01-03 10:25:14 +01:00
Ryan Mulligan
ec29bb50bf
Merge pull request #76208 from r-ryantm/auto-update/bcftools 
bcftools: 1.9 -> 1.10.2
 2020-01-02 16:42:27 -08:00
Frederik Rietdijk
6d059becd3 Merge gcc-9 into staging (#68029) 2019-12-30 16:38:38 +01:00
Merijn Broeren
133103d709
treewide: replace make/build/configure/patchFlags with nix lists 2019-12-30 12:58:11 +01:00
Franz Pletz
a88fc6be6d
strelka: fix build w/ gcc9 2019-12-30 03:18:19 +01:00
Frederik Rietdijk
eda01862c4
Merge pull request #75900 from jbedo/tebreak 
Tebreak, minia, last, bx-python, python-lzo
 2019-12-29 10:24:31 +01:00
Justin Bedo
11460d4cac
tebreak: init at 1.0 2019-12-29 17:16:10 +11:00
Franz Pletz
77b6c3cd06
Merge remote-tracking branch 'origin/master' into gcc-9 2019-12-26 14:17:36 +01:00
R. RyanTM
c905a6da5a bcftools: 1.9 -> 1.10.2 2019-12-22 20:00:29 -08:00
Justin Bedo
2191912274
minia: init at 3.2.1 2019-12-20 11:27:04 +11:00
Justin Bedo
6741cff527
last: init at 1042 2019-12-20 11:27:02 +11:00
Justin Bedo
28a057a56b
bedtools: 2.29.1 -> 2.29.2 2019-12-18 10:39:25 +11:00
Mario Rodas
5e5ce79db4
Merge pull request #75807 from jbedo/strelka 
strelka: fix broken build
 2019-12-16 23:52:35 -05:00
Justin Bedo
c3f09c33eb
strelka: fix broken build 2019-12-17 11:20:32 +11:00
Justin Bedo
50fbca4bfc
bedtools: fix clang builds 2019-12-11 09:27:57 +11:00
Justin Bedo
592d288aa2
bedtools: 2.29.0 -> 2.29.1 2019-12-10 13:24:27 +11:00
Renato Alves
e18fb092f1 kssd: init at 1.0 2019-12-08 16:48:59 +01:00
scalavision
3dfabd6eff svaba: init at 1.1.0 2019-12-08 14:51:05 +01:00
Mario Rodas
835705d11b
Merge pull request #75095 from tbenst/bftools 
bftools: 5.9.2 -> 6.3.0
 2019-12-07 03:06:00 -05:00
Tyler Benster
2700559bdc bftools: 5.9.2 -> 6.3.0 2019-12-06 02:11:00 -08:00
R. RyanTM
605e88517b paml: 4.9i -> 4.9j 2019-12-01 18:43:58 +01:00
R. RyanTM
da09e1e772 kallisto: 0.46.0 -> 0.46.1 (#74430) 2019-11-30 21:12:54 +01:00
R. RyanTM
98e0ead3ba picard-tools: 2.21.1 -> 2.21.3 (#74528) 2019-11-30 16:24:44 +01:00
R. RyanTM
6563dd3351 hmmer: 3.2.1 -> 3.3 2019-11-27 18:40:23 -08:00
Kai Wohlfahrt
6b2504f9f2 freebayes: 2017-08-23 -> 1.3.1 (2019-06-03) 2019-11-20 09:10:31 -08:00
Ben Darwin
736860d34b nifticlib and niftseg: change platform from linux to unix since these build on OSX 2019-11-14 21:25:10 -05:00
Franz Pletz
8dca8b9ccb
Merge remote-tracking branch 'origin/master' into gcc-9 2019-11-05 01:07:22 +01:00
scalavision
d9b40f6397 deeptools: init at 3.3.1 2019-11-04 02:42:36 -08:00
Franz Pletz
6b10b78872
Merge remote-tracking branch 'origin/master' into gcc-9 2019-11-03 14:44:12 +01:00
Franz Pletz
8e63a6cd13
niftyreg: fix build with gcc9 2019-11-03 14:43:37 +01:00
R. RyanTM
28b0a6a9e0 star: 2.7.2b -> 2.7.3a 2019-11-03 10:23:05 +01:00
Franz Pletz
e39773fe5b
megahit: 1.1.4 -> 1.2.9 2019-11-02 15:53:57 +01:00
Ben Darwin
ddc2955ad9 EZminc: 2017-08-29 -> 2019-07-25; mark unbroken 2019-10-26 09:55:30 -07:00
scalavision
535a7006ea truvari: init at 1.3.2 (#70877) 
pythonPackages.pyvcf: init at 0.6.8
 2019-10-24 17:06:42 -04:00
R. RyanTM
b8acb48b24 picard-tools: 2.20.8 -> 2.21.1 (#71748) 
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
 2019-10-23 09:34:40 +02:00
R. RyanTM
a9551de99a dcm2niix: 1.0.20190410 -> 1.0.20190902 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/dcm2niix/versions
 2019-10-22 16:31:19 -07:00
Renaud
e6f99fa3b1
Merge pull request #69961 from r-ryantm/auto-update/star 
star: 2.7.1a -> 2.7.2b
 2019-10-13 17:10:23 +02:00
scalavision
3d860972ee delly: init at 0.8.1 (#70871) 2019-10-10 22:08:45 -04:00
Linus Heckemann
5aa4b19946 treewide: mark some broken packages as broken 
Refs:
e6754980264fe927320d5ff2dbd24ca4fac9a160
1e9cc5b9844ef603fe160e9f671178f96200774f
793a2fe1e8bb886ca2096c5904e1193dc3268b6d
c19cf65261639f749012454932a532aa7c681e4b
f6544d618f30fae0bc4798c4387a8c7c9c047a7c
 2019-10-08 17:14:26 +02:00
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 
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
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 
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
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 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
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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
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/star/versions
 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 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
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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
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
 2019-01-28 17:17:30 +00:00
R. RyanTM
b2a7ef628a picard-tools: 2.18.21 -> 2.18.23 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
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 2019-01-16 21:43:19 -08:00
R. RyanTM
26b492b207 minimap2: 2.10 -> 2.14 (#52845) 
Semi-automatic update generated by
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based on information from
https://repology.org/metapackage/minimap2/versions
 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 
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
 2019-01-03 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 
Semi-automatic update generated by
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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
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
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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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based on information from
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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
Semi-automatic update generated by
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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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based on information from
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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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based on information from
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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
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
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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
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
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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
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
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 
Semi-automatic update generated by
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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 
Semi-automatic update generated by
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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 
Semi-automatic update generated by
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 2018-08-17 01:23:03 -07:00
R. RyanTM
ff7d82d405 picard-tools: 2.18.10 -> 2.18.11 
Semi-automatic update generated by
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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