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729 Commits

Author SHA1 Message Date
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 
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 
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 
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 
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 
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 
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 
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 
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 
last: 1179 -> 1256
 2021-10-22 08:37:19 +03:00
Justin Bedő
4e83abb0cb
Merge pull request #142199 from jbedo/picard 
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 
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 
nimpackages / buildNimPackage
 2021-09-22 18:35:38 +00:00
figsoda
0e575a459e
Merge pull request #137974 from r-ryantm/auto-update/bowtie 
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 
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 
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