R. RyanTM
4c6c40d96a
kallisto: 0.46.1 -> 0.46.2
...
Co-authored-by: Daniel Schaefer <git@danielschaefer.me>
2020-02-15 22:39:58 +01:00
Dmitry Kalinkin
5f2a3bef33
Merge pull request #79778 from jbedo/delly
...
delly: 0.8.1 -> 0.8.2
2020-02-11 03:54:02 -05:00
Justin Bedo
a8fe9e7aff
delly: 0.8.1 -> 0.8.2
...
Backported patch required for htslib 1.10.2
2020-02-11 19:21:59 +11:00
Ryan Mulligan
b99e12f4fe
Merge pull request #79534 from r-ryantm/auto-update/last
...
last: 1045 -> 1047
2020-02-10 18:10:08 -08:00
Ben Darwin
39f0e3b32b
minc_tools: enable building conversion tools
2020-02-10 19:53:25 +01:00
Ben Darwin
bcad453bcf
minc_tools: 2017-09-11 -> unstable-2019-12-04
2020-02-10 19:53:25 +01:00
R. RyanTM
dae266aa66
last: 1045 -> 1047
2020-02-08 13:04:53 +00:00
R. RyanTM
d5404eebe9
picard-tools: 2.21.6 -> 2.21.8
2020-02-07 17:20:58 +00:00
Frederik Rietdijk
419bc0a4cd
Revert "Revert "Merge master into staging-next""
...
In 87a19e9048ac241fb7a50be87c79790be87c7979
2020-02-05 19:41:25 +01:00
Frederik Rietdijk
0be87c7979
Revert "Merge master into staging-next"
...
I merged master into staging-next but accidentally pushed it to master.
This should get us back to 87a19e9048ac241fb7a576a439239e
2020-02-05 19:18:35 +01:00
R. RyanTM
3c54ae5679
SPAdes: 3.13.1 -> 3.14.0
2020-02-04 16:40:50 +00:00
R. RyanTM
42fff82421
seaview: 4.7 -> 5.0
2020-01-30 08:26:52 +00:00
Silvan Mosberger
80a2740991
Merge pull request #78265 from Synthetica9/https-homepages
...
treewide: fix redirected urls
2020-01-27 15:00:53 +01:00
Justin Bedo
7f142260d3
manta: init 1.6.0
2020-01-24 02:02:19 -08:00
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:
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
