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432 Commits

Author SHA1 Message Date
Ryan Mulligan
a6dc361cae
Merge pull request #78261 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.21.3 -> 2.21.6
 2020-01-22 16:18:57 -08:00
Patrick Hilhorst
593e11fd94
treewide: fix redirected urls 
According to https://repology.org/repository/nix_unstable/problems, we have a
lot of packages that have http links that redirect to https as their homepage.
This commit updates all these packages to use the https links as their
homepage.

The following script was used to make these updates:

```

curl https://repology.org/api/v1/repository/nix_unstable/problems \
    | jq '.[] | .problem' -r \
    | rg 'Homepage link "(.+)" is a permanent redirect to "(.+)" and should be updated' --replace 's@$1@$2@' \
    | sort | uniq > script.sed

find -name '*.nix' | xargs -P4 -- sed -f script.sed -i
```
 2020-01-22 11:26:22 +01:00
R. RyanTM
fff7a7a862 picard-tools: 2.21.3 -> 2.21.6 2020-01-22 10:12:28 +00:00
Jonathan Ringer
4de137a77d samtools: 1.9 -> 1.10 2020-01-19 13:13:01 -08:00
Jonathan Ringer
5961f211f3 python.pkgs wide: fix problematic urls 2020-01-10 21:02:12 -08:00
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:
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