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:
e675498026
1e9cc5b984
793a2fe1e8
c19cf65261
f6544d618f
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
https://repology.org/metapackage/igv/versions
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
https://repology.org/metapackage/minimap2/versions
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
https://repology.org/metapackage/picard-tools/versions
2019-01-16 21:43:19 -08:00
R. RyanTM
26b492b207
minimap2: 2.10 -> 2.14 ( #52845 )
...
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
2019-01-13 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
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/igv/versions
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
https://repology.org/metapackage/picard-tools/versions
2018-12-14 16:27:07 -08:00
R. RyanTM
87481c2ff1
star: 2.6.1c -> 2.6.1d
...
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
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
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
* 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
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/igv/versions
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
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/star/versions
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
https://repology.org/metapackage/bowtie2/versions
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
https://repology.org/metapackage/picard-tools/versions
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
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
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
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/bowtie2/versions .
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
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/igv/versions .
2018-08-17 01:23:03 -07:00
R. RyanTM
ff7d82d405
picard-tools: 2.18.10 -> 2.18.11
...
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 .
2018-08-16 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