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687 Commits

Author SHA1 Message Date
adisbladis
fcf5397793
Merge pull request #135905 from dukc/secondDmd2097 
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 
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 
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 
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 
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 
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 
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 
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
R. RyanTM
089915f634 bowtie2: 2.4.3 -> 2.4.4 2021-05-26 23:43:08 -07:00
Stéphan Kochen
c47425a230 sambamba: fix darwin build 2021-05-22 20:56:09 +02:00
Stéphan Kochen
20f36556dc samblaster: fix darwin build 2021-05-18 13:41:51 +02:00
Sandro
83c5d21320
Merge pull request #123083 from stephank/fix-est-sfs-darwin 
est-sfs: fix darwin build
 2021-05-17 18:58:33 +02:00
R. RyanTM
9528bf9fd9 bowtie2: 2.4.2 -> 2.4.3 2021-05-16 02:53:03 -04:00
Stéphan Kochen
d707979a73 est-sfs: fix darwin build 2021-05-15 12:10:05 +02:00
Stéphan Kochen
2adca7ae14
cd-hit: fix darwin build (#123026) 2021-05-14 17:27:16 -04:00
Justin Bedo
40eeb2c6d3
octopus: 0.7.3 -> 0.7.4 2021-05-11 08:46:00 +10:00
Luke Granger-Brown
884cf29501 dcm2niix: 1.0.20201102 -> 1.0.20210317 2021-05-02 11:10:40 +00:00
R. RyanTM
ad5f251230 dcm2niix: 1.0.20200331 -> 1.0.20201102 2021-05-02 03:14:11 +00:00
Justin Bedo
def7c82f88
octopus: 0.7.1 -> 0.7.3 2021-04-20 10:13:25 +10:00
Sandro
28fb287d4b
Merge pull request #118610 from GregorySchwartz/init/macs2 2021-04-14 21:15:38 +02:00
Gregory W. Schwartz
b7763a8287 macs2: init at 2.2.7.1 
Update pkgs/applications/science/biology/macs2/default.nix

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>

Update pkgs/applications/science/biology/macs2/default.nix

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>

Update pkgs/applications/science/biology/macs2/default.nix

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>

Update pkgs/applications/science/biology/macs2/default.nix

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>

Renamed package, updated version, set pypi, and added import test.

Update pkgs/applications/science/biology/MACS2/default.nix

Co-authored-by: Sandro <sandro.jaeckel@gmail.com>

Add comment about error for checking.

Two spaces indent.
 2021-04-14 10:17:53 -04:00
Gregory Schwartz
9bf867612d
meme-suite: init at 5.1.1 (#118603) 
Co-authored-by: Sandro <sandro.jaeckel@gmail.com>
 2021-04-05 22:43:27 +02:00
Sandro Jäckel
3453b89f4b
lzma: deprecate alias 2021-04-04 19:49:52 +02:00
Ryan Mulligan
f3262c2a3e
Merge pull request #117648 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.25.0 -> 2.25.1
 2021-03-29 16:10:25 -07:00
Justin Bedo
76bd953162 bedops: init 2.4.39 2021-03-28 22:27:51 -04:00
R. RyanTM
49e4c1e323 picard-tools: 2.25.0 -> 2.25.1 2021-03-26 03:16:44 +00:00
Frederik Rietdijk
5a5cb718a5 bedtools: use python3 2021-03-25 10:42:32 +01:00
Frederik Rietdijk
2c00aed6b1 bcftools: use python3 2021-03-25 10:39:47 +01:00
Bruno Bzeznik
f0eef16f9c SPAdes: 3.15.1 -> 3.15.2 + fix license and platform 2021-03-23 10:51:01 +01:00
Jan Tojnar
2445e9a681
Merge branch 'master' into staging-next 2021-03-18 19:24:39 +01:00
Thomas Mader
09acdfde94
sambamba: 0.7.1 -> 0.8.0 
Getting rid of dmd dependency and compile with ldc
 2021-03-18 17:41:30 +02:00
Martin Weinelt
0241873f7f
Merge branch 'master' into staging-next 2021-03-14 17:35:32 +01:00
Ryan Mulligan
0e63a1bb33
Merge pull request #115579 from r-ryantm/auto-update/stacks 
stacks: 2.53 -> 2.55
 2021-03-14 07:47:22 -07:00
Ryan Mulligan
03754f91eb
Merge pull request #115574 from r-ryantm/auto-update/SPAdes 
SPAdes: 3.14.1 -> 3.15.1
 2021-03-14 07:46:58 -07:00
github-actions[bot]
aea4725648
Merge master into staging-next 2021-03-10 12:21:24 +00:00
Justin Bedo
4e1a560ae4
octopus: 0.7.0 -> 0.7.1 2021-03-10 08:44:18 +11:00
R. RyanTM
cb9f13c609 stacks: 2.53 -> 2.55 2021-03-09 17:19:55 +00:00
R. RyanTM
95d96bbfe5 SPAdes: 3.14.1 -> 3.15.1 2021-03-09 17:01:01 +00:00
github-actions[bot]
5c2a7abde7
Merge master into staging-next 2021-03-08 18:22:56 +00:00
R. RyanTM
12cde5ea85 messer-slim: 3.2.1 -> 3.6 2021-03-04 18:40:37 +00:00
Robert Schütz
54757b35c1 Merge branch 'staging-next' into staging 2021-02-26 10:56:17 +01:00
Frederik Rietdijk
c456a2512f Merge master into staging-next 2021-02-26 10:25:13 +01:00
R. RyanTM
615ff1b2ab star: 2.7.7a -> 2.7.8a 2021-02-23 10:38:00 +00:00
github-actions[bot]
ed07c63105
Merge staging-next into staging 2021-02-22 06:17:08 +00:00
github-actions[bot]
227aa2c9b0
Merge master into staging-next 2021-02-22 06:17:05 +00:00
R. RyanTM
ff27c8e0ad last: 1178 -> 1179 2021-02-21 21:24:17 +00:00
Ben Siraphob
127733211e
treewide: unzip buildInputs to nativeBuildInputs (#112302) 2021-02-20 16:01:53 -05:00
github-actions[bot]
abe7db36a4
Merge staging-next into staging 2021-02-20 00:36:40 +00:00
Ben Siraphob
223f25cf4a treewide: add targetPrefix to hardcoded references to CC=cc 2021-02-20 01:01:46 +07:00
Ben Siraphob
e03c068af5 treewide: makeWrapper buildInputs to nativeBuildInputs 2021-02-19 20:09:16 +07:00
github-actions[bot]
318f95e4c2
Merge master into staging-next 2021-02-13 06:16:33 +00:00
R. RyanTM
d1067751c6 picard-tools: 2.24.2 -> 2.25.0 2021-02-11 21:10:44 +00:00
github-actions[bot]
30dddce5e8
Merge master into staging-next 2021-02-09 06:16:02 +00:00
Mario Rodas
f9a095da28
Merge pull request #112191 from r-ryantm/auto-update/star 
star: 2.7.6a -> 2.7.7a
 2021-02-08 20:17:49 -05:00
github-actions[bot]
1c86cb40e9
Merge master into staging-next 2021-02-08 00:36:16 +00:00
Ryan Mulligan
64c446d0ba
Merge pull request #112021 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.24.1 -> 2.24.2
 2021-02-07 14:57:32 -08:00
github-actions[bot]
aaaf1218bf
Merge master into staging-next 2021-02-07 00:37:36 +00:00
R. RyanTM
ef6ed50cb4 star: 2.7.6a -> 2.7.7a 2021-02-06 19:50:22 +00:00
Orivej Desh
8d0af26e1d blast: 2.10.0 -> 2.11.0 
Fixes build with gcc10.
 2021-02-06 19:20:56 +00:00
R. RyanTM
0adfe0f108 picard-tools: 2.24.1 -> 2.24.2 2021-02-05 12:35:00 +00:00
Justin Bedo
6d84ba18d5
bowtie2: resolve missing runtime dependencies 2021-02-03 11:12:26 +11:00
R. RyanTM
ad28c0fb42 last: 1170 -> 1178 2021-01-30 07:52:29 +00:00
Phillip Cloud
bba47f95f1 sortmerna: mark broken on darwin 2021-01-26 12:55:33 -05:00
Pavol Rusnak
a6ce00c50c
treewide: remove stdenv where not needed 2021-01-25 18:31:47 +01:00
Sandro
ad445d3728
Merge pull request #110735 from jbedo/bedtools 
bedtools: 2.29.2 -> 2.30.0
 2021-01-25 11:04:30 +01:00
Ryan Mulligan
afebf1cc9a
Merge pull request #110529 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.24.0 -> 2.24.1
 2021-01-24 18:06:28 -08:00
Justin Bedo
d81e79af15
bedtools: 2.29.2 -> 2.30.0 2021-01-25 13:06:22 +11:00
volth
bc0d605cf1 treewide: fix double quoted strings in meta.description 
Signed-off-by: Ben Siraphob <bensiraphob@gmail.com>
 2021-01-24 19:56:59 +07:00
Pavol Rusnak
90f7338112
treewide: stdenv.lib -> lib 2021-01-24 01:49:49 +01:00
Markus Kowalewski
6dba41fbcb
mpi: use mpi attribute consistently as the default MPI implementations 
Use the attribute mpi to provide a system wide default MPI
implementation. The default is openmpi (as before).
This now allows for overriding the MPI implentation by using
the overlay mechanism. Build all packages with mpich instead
of the default openmpi can now be achived like this:
self: super:
 {
   mpi = super.mpich;
 }

All derivations that have been using "mpi ? null" to provide optional
building with MPI have been change in the following way to allow for
optional builds with MPI:
{ ...
, mpi
, useMpi ? false
}
 2021-01-23 12:15:13 +01:00
R. RyanTM
e1ea0a237a picard-tools: 2.24.0 -> 2.24.1 2021-01-22 19:10:27 +00:00
zowoq
932941b79c treewide: editorconfig fixes 
- remove trailing whitespace
- use spaces for indentation
 2021-01-21 13:29:54 +10:00
R. RyanTM
427bbe059a picard-tools: 2.23.9 -> 2.24.0 2021-01-20 20:42:01 +00:00
zowoq
759a2cd563 ecopcr: use spaces for indentation 2021-01-20 10:53:10 +10:00
zowoq
31f5dd3f36 treewide: editorconfig fixes 
- remove trailing whitespace
- use spaces for indentation
 2021-01-20 09:11:11 +10:00
Jonathan Ringer
9bb3fccb5b treewide: pkgs.pkgconfig -> pkgs.pkg-config, move pkgconfig to alias.nix 
continuation of #109595

pkgconfig was aliased in 2018, however, it remained in
all-packages.nix due to its wide usage. This cleans
up the remaining references to pkgs.pkgsconfig and
moves the entry to aliases.nix.

python3Packages.pkgconfig remained unchanged because
it's the canonical name of the upstream package
on pypi.
 2021-01-19 01:16:25 -08:00
Jonathan Ringer
200bb8c977 cd-hit: remove non-existent package 2021-01-19 01:16:25 -08:00