R. Ryantm
1e7c64aae1
bcftools: 1.14 -> 1.15
2022-02-25 11:12:05 -08:00
R. Ryantm
ce9d28cc49
picard-tools: 2.26.10 -> 2.26.11
2022-02-24 17:34:18 +00:00
Scriptkiddi
4e60a4823b
febio-studio: init at 1.6.1
2022-02-21 16:43:36 +01:00
R. RyanTM
94f61e4c82
SPAdes: 3.15.3 -> 3.15.4
...
(#158938 )
2022-02-18 00:55:34 +01:00
R. Ryantm
240262f564
messer-slim: 3.7 -> 3.7.1
2022-02-14 00:46:29 +00:00
Justin Bedő
2759d6f8d8
Merge pull request #159675 from r-ryantm/auto-update/picard-tools
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picard-tools: 2.26.9 -> 2.26.10
2022-02-13 09:53:20 +11:00
Justin Bedő
7ff9c00c4b
Merge pull request #159562 from r-ryantm/auto-update/mosdepth
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mosdepth: 0.3.2 -> 0.3.3
2022-02-13 09:27:54 +11:00
R. Ryantm
8a4946df2d
picard-tools: 2.26.9 -> 2.26.10
2022-02-12 22:20:29 +00:00
R. Ryantm
8bb7bc766f
mosdepth: 0.3.2 -> 0.3.3
2022-02-12 14:31:47 +00:00
R. Ryantm
6ca5bb6e20
last: 1256 -> 1260
2022-02-12 02:52:18 +00:00
Renaud
2ddcc2b369
hisat2: update homepage
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and use SPDX 3.0 license identifier
2022-02-06 15:10:53 +01:00
R. Ryantm
d44e044d84
kallisto: 0.46.2 -> 0.48.0
2022-01-31 09:53:54 -08:00
Bruno Bzeznik
b6fa4975cf
repseek: init at 9Sep2014 ( #148017 )
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Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
2022-01-31 14:59:32 +01:00
markuskowa
01f1b41a7d
Merge pull request #156381 from r-ryantm/auto-update/bowtie2
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bowtie2: 2.4.4 -> 2.4.5
2022-01-29 14:56:23 +01:00
R. RyanTM
8bd7d6d6e0
star: 2.7.9a -> 2.7.10a
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(#155868 )
2022-01-24 19:51:44 +01:00
R. Ryantm
ebb9e86bf9
bowtie2: 2.4.4 -> 2.4.5
2022-01-23 22:45:59 +00:00
Mario Rodas
111d7dc831
Merge pull request #156014 from r-ryantm/auto-update/deeptools
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deeptools: 3.5.0 -> 3.5.1
2022-01-22 23:45:09 -05:00
Justin Bedő
c24af4642c
sambamba: 0.8.1 -> 0.8.2 ( #155972 )
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Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
2022-01-23 04:51:46 +01:00
R. Ryantm
227011af59
deeptools: 3.5.0 -> 3.5.1
2022-01-21 05:36:24 +00:00
Frederik Rietdijk
afef6d0e81
Merge pull request #154687 from dotlambda/python-alias
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python,pythonPackages: make aliases
2022-01-17 09:37:49 +01:00
R. RyanTM
4fa7c297f2
minimap2: 2.23 -> 2.24
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* minimap2: 2.23 -> 2.24 (#153189 )
* minimap2: no support for aarch64
Co-authored-by: Renaud <c0bw3b@users.noreply.github.com>
2022-01-17 08:49:35 +01:00
Robert Schütz
d5cceedbd1
python,pythonPackages: make aliases
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Since aliases are disallowed in nixpkgs, this makes usage of Python 2
which is EOL more explicit.
2022-01-16 18:39:59 +00:00
Robert Schütz
65e959eb9a
tebreak: also use python3 for tests
2022-01-16 18:00:59 +00:00
Martin Weinelt
492e5e07c9
lumpy: drop
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Removed because it requires python2 and the upstream repository looks
undermaintained.
2022-01-16 02:36:23 +01:00
markuskowa
09819d7eff
Merge pull request #152801 from r-ryantm/auto-update/messer-slim
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messer-slim: 3.6 -> 3.7
2022-01-03 10:50:18 +01:00
R. RyanTM
e4992cdd65
stacks: 2.59 -> 2.60
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(#149101 )
2022-01-02 19:23:58 +01:00
Martin Weinelt
4beaf5301d
python3Packages.xenomapper: move to top-level
2022-01-01 02:09:11 +01:00
R. Ryantm
37d2f5cbb4
messer-slim: 3.6 -> 3.7
2021-12-30 20:32:56 +00:00
Bobby Rong
4fdcad0d6b
Merge pull request #149379 from r-ryantm/auto-update/minimap2
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minimap2: 2.22 -> 2.23
2021-12-27 18:05:04 +08:00
Felix Buehler
e578d45c10
diamond: switch to fetchFromGitHub
2021-12-23 19:11:17 +01:00
Felix Buehler
865eee2b26
kssd: switch to fetchFromGitHub
2021-12-23 19:11:17 +01:00
Felix Buehler
2f4a86e7d7
messer-slim: switch to fetchFromGitHub
2021-12-23 19:11:17 +01:00
Felix Buehler
e1bd890fb0
niftyseg: switch to fetchFromGitHub
2021-12-23 19:11:17 +01:00
Justin Bedo
fa6244b712
picard-tools: 2.26.6 -> 2.26.9
2021-12-22 22:20:36 +11:00
Justin Bedő
f6e14b6ada
Merge pull request #150628 from jbedo/subread
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subread: init 2.0.3
2021-12-15 13:46:45 +11:00
Justin Bedo
6a1f4a51eb
subread: init 2.0.3
2021-12-14 13:30:23 +11:00
R. Ryantm
d4a5bdc264
seaview: 5.0.4 -> 5.0.5
2021-12-12 15:59:16 +00:00
R. Ryantm
d337b164d6
minimap2: 2.22 -> 2.23
2021-12-07 15:04:36 +00:00
Justin Bedő
711ef56370
Merge pull request #148514 from jbedo/picard
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picard-tools: 2.26.4 -> 2.26.6
2021-12-05 06:56:25 +11:00
Justin Bedo
17e3b75414
picard-tools: 2.26.4 -> 2.26.6
2021-12-04 07:51:31 +11:00
Justin Bedo
1a768ef4da
genmap: init 1.3.0
2021-12-04 06:51:16 +11:00
Justin Bedo
82aef7957d
fastp: 0.23.1 -> 0.23.2
2021-12-02 08:03:17 +11:00
Vikram Narayanan
b1d95dca56
mrtrix: 3.0.2 -> unstable-2021-11-25
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The latest stable version fails to build with latest eigen (> 3).
https://github.com/MRtrix3/mrtrix3/pull/2368
2021-11-30 21:03:53 -08:00
Sergei Trofimovich
8147fb683c
samtools: pull upstream fix for ncurses-6.3
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Without the fix build on ncurses-6.3 fails as:
bam_tview_curses.c:88:5: error: format not a string literal and no format arguments [-Werror=format-security]
88 | mvprintw(y,x,str);
| ^~~~~~~~
2021-11-26 13:02:05 +00:00
Justin Bedo
c1eb0dddea
delly: 0.8.7 -> 0.9.1
2021-11-25 21:19:48 +11:00
Robert Scott
ec24bab90e
hmmer: restrict platforms to x86_64
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technically big-endian powerpc with VMX is also supported, but
on x86, SSE is apparently *required* which means we can't build
a pure i686 version
2021-11-20 19:17:57 +00:00
Mario Rodas
c8fb7191ad
Merge pull request #143541 from r-ryantm/auto-update/bcftools
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bcftools: 1.13 -> 1.14
2021-11-14 21:14:30 -05:00
Bruno Bzeznik
4e5a245894
obitools3: removed useless python restriction
2021-11-08 07:51:48 +01:00
Felix Buehler
b52ab3b712
pkgs/applications: rename name to pname&version part 2
2021-11-07 14:53:06 +01:00
Justin Bedő
a5ac0a33a7
Merge pull request #144529 from r-ryantm/auto-update/picard-tools
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picard-tools: 2.26.3 -> 2.26.4
2021-11-04 07:19:02 +11:00
R. Ryantm
509a8c298f
picard-tools: 2.26.3 -> 2.26.4
2021-11-03 19:57:00 +00:00
Bruno Bzeznik
0d9ec2d3f0
obitools3: fix build on aarch64 + formatting
2021-11-03 11:59:05 +02:00
R. Ryantm
6282512ef7
dcm2niix: 1.0.20210317 -> 1.0.20211006
2021-10-29 09:34:20 +00:00
R. Ryantm
5f6bd8187b
bcftools: 1.13 -> 1.14
2021-10-29 02:49:14 +00:00
Artturi
493094366b
Merge pull request #142164 from jbedo/last
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last: 1179 -> 1256
2021-10-22 08:37:19 +03:00
Justin Bedő
4e83abb0cb
Merge pull request #142199 from jbedo/picard
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picard-tools: 2.26.2 -> 2.26.3
2021-10-22 14:36:28 +11:00
Justin Bedo
f120d4daf4
picard-tools: 2.26.2 -> 2.26.3
2021-10-19 21:24:56 +11:00
Justin Bedo
08489c40ab
fastp: 0.22.0 -> 0.23.1
2021-10-19 21:09:05 +11:00
Justin Bedo
f7414542d0
last: 1179 -> 1256
2021-10-19 13:23:14 +11:00
Justin Bedo
02a1a2b3c8
samtools: 1.11 -> 1.13
2021-10-12 10:19:36 +11:00
figsoda
3109ff5765
treewide: avoid use of lib.optional with list in inputs
2021-10-04 13:02:42 -04:00
R. RyanTM
5becb56f71
star: 2.7.8a -> 2.7.9a
2021-09-24 10:37:28 +08:00
Bobby Rong
c25465873c
Merge pull request #138022 from natsukium/blast/update
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blast: 2.11.0 -> 2.12.0
2021-09-23 14:48:35 +08:00
Guillaume Girol
4bc83aaffa
Merge pull request #136489 from ehmry/nimPackages
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nimpackages / buildNimPackage
2021-09-22 18:35:38 +00:00
figsoda
0e575a459e
Merge pull request #137974 from r-ryantm/auto-update/bowtie
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bowtie: 1.3.0 -> 1.3.1
2021-09-17 22:52:43 -04:00
Bobby Rong
12d38c57c3
Merge pull request #134133 from Kranzes/auto-update/SPAdes
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SPAdes: 3.15.2 -> 3.15.3
2021-09-16 17:09:24 +08:00
Tomoya Otabi
1e9bd43214
blast: 2.11.0 -> 2.12.0
2021-09-15 15:33:44 +00:00
R. RyanTM
7bf7c9b92b
bowtie: 1.3.0 -> 1.3.1
2021-09-15 07:35:44 +00:00
R. RyanTM
e676fdcb90
picard-tools: 2.26.0 -> 2.26.2
2021-09-14 19:53:25 +00:00
adisbladis
fcf5397793
Merge pull request #135905 from dukc/secondDmd2097
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D compiler update
2021-09-13 11:36:55 -05:00
Sandro
205c2ada66
Merge pull request #136967 from bzizou/obitools
2021-09-11 16:27:18 +02:00
Bruno Bzeznik
3bd1b0ed0d
obitools3: 3.0.0-beta14 -> 3.0.1b11
2021-09-07 09:38:41 +02:00
Emery Hemingway
323c503cba
mosdepth: convert to buildNimPackage
2021-09-05 11:20:02 +02:00
Ate Eskola
b2a39efa57
sambamba 0.8.0 -> 0.8.1
2021-08-31 12:37:49 +03:00
davidak
1b78608c69
Merge pull request #135516 from bzizou/stacks
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stacks: Changed license to gpl3Plus
2021-08-26 03:50:48 +02:00
Justin Bedo
b1b57ec04e
fastp: 0.20.1 -> 0.22.0
2021-08-25 09:52:07 +10:00
Ryan Mulligan
8c2e2ffe95
Merge pull request #135212 from r-ryantm/auto-update/stacks
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stacks: 2.55 -> 2.59
2021-08-24 09:03:17 -07:00
Bruno Bzeznik
a240cd9f4f
stacks: Changed license to gpl3Plus
2021-08-24 09:47:24 +02:00
Ryan Mulligan
997f4452a4
Merge pull request #135255 from r-ryantm/auto-update/picard-tools
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picard-tools: 2.25.7 -> 2.26.0
2021-08-23 20:56:38 -07:00
Jörg Thalheim
11e5c3ac4b
bowtie: fix homepage
2021-08-22 16:08:28 +02:00
R. RyanTM
742cd80071
picard-tools: 2.25.7 -> 2.26.0
2021-08-22 10:47:38 +00:00
R. RyanTM
67c1256ddd
stacks: 2.55 -> 2.59
2021-08-22 07:08:39 +00:00
Sebastián Mancilla
8f94a33b38
treewide: ensure pre/post phase hooks are strings
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Some derivations use lib.optional or lib.optionals when setting pre/post
phase hooks. Ensure the proper lib.optionalString is used.
2021-08-20 19:08:42 -04:00
Ryan Mulligan
ad59a67ec0
Merge pull request #134444 from r-ryantm/auto-update/picard-tools
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picard-tools: 2.25.1 -> 2.25.7
2021-08-17 16:47:31 -07:00
R. RyanTM
1a23a8bb9e
picard-tools: 2.25.1 -> 2.25.7
2021-08-17 13:50:42 +00:00
Ilan Joselevich
9f5b3fafa0
SPAdes: 3.15.2 -> 3.15.3
2021-08-15 11:12:42 +03:00
R. RyanTM
5693a554e2
minimap2: 2.17 -> 2.22
2021-08-14 15:55:35 +00:00
Artturi
e69c8ea78e
Merge pull request #111691 from jbedo/bowtie2
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bowtie2: resolve missing runtime dependencies
2021-08-07 04:03:47 +03:00
Sandro
04b5e62d8d
Merge pull request #132468 from Stunkymonkey/applications-phases1
2021-08-05 09:37:57 +02:00
Felix Buehler
be219752d2
picard-tools: deprecate phases
2021-08-03 00:04:29 +02:00
Felix Buehler
4b883542fe
varscan: deprecate phases
2021-08-03 00:04:16 +02:00
Artturin
f173c77476
perlPackages.ImageMagick: rename from perlPackages.PerlMagick
2021-08-02 20:05:00 +03:00
Sandro
1524f36b3e
Merge pull request #131627 from jbedo/mosdepth
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mosdepth: 0.3.1 -> 0.3.2
2021-07-29 13:56:24 +00:00
Sandro Jäckel
cebfbdff37
mrbayes: 3.2.7 -> 3.2.7a
2021-07-27 14:30:23 +02:00
Sandro Jäckel
108ad942fb
mrbayes: modernize
2021-07-27 11:53:51 +02:00
Justin Bedo
d885373469
mosdepth: 0.3.1 -> 0.3.2
2021-07-27 09:52:22 +10:00
R. RyanTM
d943e6aa12
bedops: 2.4.39 -> 2.4.40
2021-07-23 01:02:40 +00:00
Sandro
d5bd34ebf2
treewide: convert phases that contain ":" to dont* = true ( #130500 )
2021-07-18 23:42:48 +02:00
R. RyanTM
7177212409
bcftools: 1.11 -> 1.13
2021-07-10 10:15:10 +00:00
scalavision
c6ca3545ae
truvari: 2.0.2 -> 2.1.1 ( #126839 )
...
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
2021-06-15 22:14:20 +02:00
