fff7a7a862
picard-tools: 2.21.3 -> 2.21.6
2020-01-22 10:12:28 +00:00
4de137a77d
samtools: 1.9 -> 1.10
2020-01-19 13:13:01 -08:00
5961f211f3
python.pkgs wide: fix problematic urls
2020-01-10 21:02:12 -08:00
f7a4e4a93a
bayescan: init at 2.1 ( #68191 )
...
Co-authored-by: Dmitry Kalinkin <dmitry.kalinkin@gmail.com>
2020-01-09 12:38:53 -05:00
fdfebafc10
blast: init at 2.10.0 ( #61430 )
...
Co-authored-by: Pavel Chuprikov <pschuprikov@gmail.com>
2020-01-07 20:14:18 +01:00
4bc4c70bc6
last: 1042 -> 1045
2020-01-06 11:46:28 -08:00
7aa2b0215b
Merge master into staging-next
2020-01-03 10:25:14 +01:00
ec29bb50bf
Merge pull request #76208 from r-ryantm/auto-update/bcftools
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bcftools: 1.9 -> 1.10.2
2020-01-02 16:42:27 -08:00
6d059becd3
Merge gcc-9 into staging ( #68029 )
2019-12-30 16:38:38 +01:00
133103d709
treewide: replace make/build/configure/patchFlags with nix lists
2019-12-30 12:58:11 +01:00
a88fc6be6d
strelka: fix build w/ gcc9
2019-12-30 03:18:19 +01:00
eda01862c4
Merge pull request #75900 from jbedo/tebreak
...
Tebreak, minia, last, bx-python, python-lzo
2019-12-29 10:24:31 +01:00
11460d4cac
tebreak: init at 1.0
2019-12-29 17:16:10 +11:00
77b6c3cd06
Merge remote-tracking branch 'origin/master' into gcc-9
2019-12-26 14:17:36 +01:00
c905a6da5a
bcftools: 1.9 -> 1.10.2
2019-12-22 20:00:29 -08:00
2191912274
minia: init at 3.2.1
2019-12-20 11:27:04 +11:00
6741cff527
last: init at 1042
2019-12-20 11:27:02 +11:00
28a057a56b
bedtools: 2.29.1 -> 2.29.2
2019-12-18 10:39:25 +11:00
5e5ce79db4
Merge pull request #75807 from jbedo/strelka
...
strelka: fix broken build
2019-12-16 23:52:35 -05:00
c3f09c33eb
strelka: fix broken build
2019-12-17 11:20:32 +11:00
50fbca4bfc
bedtools: fix clang builds
2019-12-11 09:27:57 +11:00
592d288aa2
bedtools: 2.29.0 -> 2.29.1
2019-12-10 13:24:27 +11:00
e18fb092f1
kssd: init at 1.0
2019-12-08 16:48:59 +01:00
3dfabd6eff
svaba: init at 1.1.0
2019-12-08 14:51:05 +01:00
835705d11b
Merge pull request #75095 from tbenst/bftools
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bftools: 5.9.2 -> 6.3.0
2019-12-07 03:06:00 -05:00
2700559bdc
bftools: 5.9.2 -> 6.3.0
2019-12-06 02:11:00 -08:00
605e88517b
paml: 4.9i -> 4.9j
2019-12-01 18:43:58 +01:00
da09e1e772
kallisto: 0.46.0 -> 0.46.1 ( #74430 )
2019-11-30 21:12:54 +01:00
98e0ead3ba
picard-tools: 2.21.1 -> 2.21.3 ( #74528 )
2019-11-30 16:24:44 +01:00
6563dd3351
hmmer: 3.2.1 -> 3.3
2019-11-27 18:40:23 -08:00
6b2504f9f2
freebayes: 2017-08-23 -> 1.3.1 (2019-06-03)
2019-11-20 09:10:31 -08:00
736860d34b
nifticlib and niftseg: change platform from linux to unix since these build on OSX
2019-11-14 21:25:10 -05:00
8dca8b9ccb
Merge remote-tracking branch 'origin/master' into gcc-9
2019-11-05 01:07:22 +01:00
d9b40f6397
deeptools: init at 3.3.1
2019-11-04 02:42:36 -08:00
6b10b78872
Merge remote-tracking branch 'origin/master' into gcc-9
2019-11-03 14:44:12 +01:00
8e63a6cd13
niftyreg: fix build with gcc9
2019-11-03 14:43:37 +01:00
28b0a6a9e0
star: 2.7.2b -> 2.7.3a
2019-11-03 10:23:05 +01:00
e39773fe5b
megahit: 1.1.4 -> 1.2.9
2019-11-02 15:53:57 +01:00
ddc2955ad9
EZminc: 2017-08-29 -> 2019-07-25; mark unbroken
2019-10-26 09:55:30 -07:00
535a7006ea
truvari: init at 1.3.2 ( #70877 )
...
pythonPackages.pyvcf: init at 0.6.8
2019-10-24 17:06:42 -04:00
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
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
e6f99fa3b1
Merge pull request #69961 from r-ryantm/auto-update/star
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star: 2.7.1a -> 2.7.2b
2019-10-13 17:10:23 +02:00
3d860972ee
delly: init at 0.8.1 ( #70871 )
2019-10-10 22:08:45 -04:00
5aa4b19946
treewide: mark some broken packages as broken
...
Refs:
e6754980264fe927320d5ff2dbd24ca4fac9a160
1e9cc5b9844ef603fe160e9f671178f96200774f
793a2fe1e8bb886ca2096c5904e1193dc3268b6d
c19cf65261639f749012454932a532aa7c681e4b
f6544d618f30fae0bc4798c4387a8c7c9c047a7c
2019-10-08 17:14:26 +02:00
1ba3f3f00f
SPAdes: init at 3.13.1 ( #63082 )
2019-10-03 09:18:48 +00:00
8519cd1aa0
Merge pull request #69735 from r-ryantm/auto-update/picard-tools
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picard-tools: 2.20.5 -> 2.20.8
2019-09-29 15:44:33 -07:00
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
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
af5176b430
Merge pull request #63117 from bzizou/macse
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macse: init at 2.03
2019-09-27 17:26:07 -04:00
e4108becbe
macse: init at 2.03
2019-09-24 08:24:07 +02:00
148c82e07e
maintainer: mimadrid: update github username and personal data
2019-09-14 12:15:46 +02:00
f6182da2c6
ants: use itk 4.x
2019-09-13 11:54:21 +02:00
7b8fb5c06c
treewide: remove redundant quotes
2019-09-08 23:38:31 +00:00
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
66bc7fc1b3
Merge master into staging-next
2019-09-06 22:46:05 +02:00
6beabe7d2c
bedtools: 2.28.0 -> 2.29.0
2019-09-06 21:23:15 +02:00
cdf426488b
Merge branch 'master' into staging-next
...
Fixed trivial conflicts caused by removing rec.
2019-09-06 03:20:09 +02:00
3f83cbf538
xenomapper: init 1.0.2
2019-09-05 20:50:22 +10:00
de85797565
Merge remote-tracking branch 'origin/master' into gcc-8
2019-09-03 22:15:07 +02:00
f21211ebfe
Merge branch 'master' into staging
2019-09-02 23:25:24 +02:00
2aa9b655f4
kallisto: 0.43.1 -> 0.46.0
2019-08-31 14:06:31 -06:00
98ef78326d
Merge staging-next into staging
2019-08-31 18:07:33 +02:00
96e5474329
Merge master into staging-next
2019-08-31 18:04:31 +02:00
a8d26fc34a
Merge pull request #63127 from bzizou/trimal
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trimal: init at 1.4.1
2019-08-31 13:04:41 +02:00
ad1d58c622
Merge staging-next into staging
2019-08-31 10:04:20 +02:00
fc74ba8291
Merge master into staging-next
2019-08-31 09:50:38 +02:00
08f68313a4
treewide: remove redundant rec
2019-08-28 11:07:32 +00:00
8a4721d606
Merge pull request #64669 from luispedro/add_sortmerna
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sortmerna: init at 3.0.3
2019-08-27 17:19:53 +02:00
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
616b8343c4
Merge remote-tracking branch 'upstream/master' into gcc-8
2019-08-25 18:55:46 +02:00
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
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
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
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
c6f1c9044b
Merge pull request #63282 from jbedo/strelka
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strelka: 2.9.5 -> 2.9.10
2019-08-01 23:44:58 +00:00
481bb449a2
Merge pull request #64897 from bzizou/est-sfs
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est-sfs: init at 2.03
2019-07-22 22:52:16 +02:00
11ed86d873
bedtools: 2.27.1 -> 2.28.0
2019-07-20 14:15:38 +02:00
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
e7920cbcfc
Merge pull request #64862 from r-ryantm/auto-update/picard-tools
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picard-tools: 2.20.2 -> 2.20.3
2019-07-16 20:04:43 -07:00
9a22c8c697
est-sfs: init at 2.03
2019-07-16 13:55:59 +02:00
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
7ce0cc0a6a
Merge pull request #64324 from jbedo/hisat2
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hisat2: fix missing perl dependency
2019-07-13 13:21:11 -04:00
508ae42a0f
treewide: fix redirect URLs
2019-07-10 12:52:51 -07:00
d2d449cea5
hisat2: fix missing perl dependency
2019-07-05 10:29:51 +10:00
a07d045b00
Merge pull request #63488 from jbedo/octopus
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octopus: init 0.6.3-beta
2019-06-27 12:43:25 +02:00
d162165350
mosdepth: 0.2.3 -> 0.2.6
2019-06-22 22:41:59 +02:00
b8b71aaaf9
octopus: init 0.6.3-beta
2019-06-19 23:09:33 +10:00
2458209c3e
dcm2niix: 1.0.20170130 -> 1.0.20190410
2019-06-18 22:12:40 +02:00
1be8ba08d3
strelka: 2.9.5 -> 2.9.10
2019-06-17 16:09:25 +10:00
394bee72db
ants: fix build with gcc8
2019-06-17 07:26:00 +02:00
f3282c8d1e
treewide: remove unused variables ( #63177 )
...
* treewide: remove unused variables
* making ofborg happy
2019-06-16 19:59:05 +00:00
aafffb2614
trimal: init at 1.4.1
2019-06-14 16:31:39 +02:00
4cb64dba39
Merge pull request #58362 from bzizou/cd-hit
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cd-hit: init at 4.8.1
2019-06-13 20:39:54 -04:00
9fbf8625f1
cd-hit: init at 4.8.1
2019-06-13 14:35:13 +02:00
48c8756157
pythonPackages.neuron: restrict to x86 platforms
2019-06-09 12:18:58 +02:00
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
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
d598eca41e
Merge pull request #62752 from matthewbauer/darwin-fixes100
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Fixes for x86_64-darwin failures on Hydra
2019-06-06 09:46:41 -04:00
441485af66
iv: only use patchelf on linux
2019-06-05 23:42:58 -04:00
R. RyanTM
Jonathan Ringer
Bruno Bzeznik
Luis Pedro Coelho
Frederik Rietdijk
Ryan Mulligan
Merijn Broeren
Franz Pletz
Frederik Rietdijk
Justin Bedo
Mario Rodas
Renato Alves
scalavision
Tyler Benster
Kai Wohlfahrt
Ben Darwin
scalavision
Renaud
Linus Heckemann
Aaron Andersen
Miguel Madrid Mencía
volth
Jan Tojnar
Vladimír Čunát
Tadeo Kondrak
Lassulus
Léo Gaspard
Robin Gloster
lewo
worldofpeace
markuskowa
royneary
Robert Scott
Matthew Bauer