JakeHillion/nixpkgs
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335 Commits

Author SHA1 Message Date
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
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