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648 commits

Author SHA1 Message Date
Justin Bedo 08489c40ab
fastp: 0.22.0 -> 0.23.1 2021-10-19 21:09:05 +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