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661 commits

Author SHA1 Message Date
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