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236 commits

Author SHA1 Message Date
R. RyanTM
27e05d81a5 star: 2.7.0a -> 2.7.0c 
Semi-automatic update generated by
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based on information from
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 2019-03-03 20:55:25 +01:00
R. RyanTM
9989b7c8c4 igv: 2.4.17 -> 2.4.19 
Semi-automatic update generated by
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based on information from
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 2019-03-03 20:48:52 +01:00
tbenst
1cb81a69a0 cmtk: init at 3.3.1 (#54016) 
* cmtk: init at 3.3.1
 2019-02-08 17:41:14 -05:00
markuskowa
0496c08afd
Merge pull request #55298 from r-ryantm/auto-update/igv 
igv: 2.4.16 -> 2.4.17
 2019-02-06 12:50:24 +01:00
R. RyanTM
da628f0cbd igv: 2.4.16 -> 2.4.17 
Semi-automatic update generated by
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based on information from
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 2019-02-05 20:06:55 -08:00
R. RyanTM
e27eaf6111 star: 2.6.1d -> 2.7.0a 
Semi-automatic update generated by
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based on information from
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 2019-02-03 17:20:27 -08:00
markuskowa
e27e114803
Merge pull request #53677 from jbedo/snpeff-4.3T 
snpeff: 4.3q -> 4.3t
 2019-01-31 10:36:32 +01:00
Justin Bedo
75dd587793
snpeff: 4.3q -> 4.3t 2019-01-31 15:15:05 +11:00
R. RyanTM
2b39f17d08 minimap2: 2.14 -> 2.15 
Semi-automatic update generated by
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based on information from
https://repology.org/metapackage/minimap2/versions
 2019-01-28 20:01:47 +00:00
R. RyanTM
00cdff318a picard-tools: 2.18.23 -> 2.18.25 
Semi-automatic update generated by
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based on information from
https://repology.org/metapackage/picard-tools/versions
 2019-01-28 17:17:30 +00:00
R. RyanTM
b2a7ef628a picard-tools: 2.18.21 -> 2.18.23 
Semi-automatic update generated by
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based on information from
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 2019-01-16 21:43:19 -08:00
R. RyanTM
26b492b207 minimap2: 2.10 -> 2.14 (#52845) 
Semi-automatic update generated by
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 2019-01-13 22:34:45 +01:00
tbenst
d34f2b9b96 bftools: init at 5.9.2 (#53769) 2019-01-10 18:28:28 -05:00
Frederik Rietdijk
2da31b80bb Merge master into staging-next 2019-01-03 20:07:35 +01:00
R. RyanTM
c00dbcb7c4 picard-tools: 2.18.20 -> 2.18.21 
Semi-automatic update generated by
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based on information from
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 2019-01-03 08:39:10 +01:00
Frederik Rietdijk
10afccf145 Merge staging-next into staging 2018-12-27 18:11:34 +01:00
R. RyanTM
338cf1a7fc igv: 2.4.15 -> 2.4.16 
Semi-automatic update generated by
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 2018-12-26 10:44:01 +01:00
Jan Tojnar
ef935fa101
Merge branch 'master' into staging 2018-12-24 15:02:29 +01:00
Renaud
6f5ec9d889
Merge pull request #52134 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.18.17 -> 2.18.20
 2018-12-19 17:53:47 +01:00
Frederik Rietdijk
9ab61ab8e2 Merge staging-next into staging 2018-12-19 09:00:36 +01:00
volth
fed7914539
Merge branch 'staging' into make-perl-pathd 2018-12-18 17:13:27 +00:00
markuskowa
96b0a38f07
Merge pull request #52015 from r-ryantm/auto-update/star 
star: 2.6.1c -> 2.6.1d
 2018-12-16 23:38:37 +01:00
volth
bb9557eb7c lib.makePerlPath -> perlPackages.makePerlPath 2018-12-15 03:50:31 +00:00
R. RyanTM
b261fb0474 picard-tools: 2.18.17 -> 2.18.20 
Semi-automatic update generated by
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based on information from
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 2018-12-14 16:27:07 -08:00
R. RyanTM
87481c2ff1 star: 2.6.1c -> 2.6.1d 
Semi-automatic update generated by
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based on information from
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 2018-12-14 01:07:34 -08:00
Maximilian Bosch
de02111a51
Merge pull request #51534 from jbedo/bowtie2 
bowtie2: fix missing dependencies
 2018-12-10 00:58:51 +01:00
Justin Bedo
8c5251e3c0
bowtie2: fix missing dependencies 2018-12-05 10:51:30 +11:00
Frederik Rietdijk
9b81c7e455 Merge staging-next into staging 2018-11-29 09:18:35 +01:00
R. RyanTM
36a0335d02 picard-tools: 2.18.14 -> 2.18.17 (#50647) 
* picard-tools: 2.18.14 -> 2.18.16

Changelog: https://github.com/broadinstitute/picard/releases/tag/2.18.16
Semi-automatic update generated by
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* picard-tools: 2.18.16 -> 2.18.17

Changelog: https://github.com/broadinstitute/picard/releases/tag/2.18.17
 2018-11-27 14:31:09 +01:00
Matthew Bauer
d492f53faf
Merge pull request #50527 from matthewbauer/ninja-check-phase 
Add check phase to ninja setup hook
 2018-11-20 16:55:12 -06:00
Matthew Bauer
2c47a4229f treewide: remove ctest usages 
These are already in the generated makefiles!
 2018-11-18 19:31:02 -06:00
Ben Darwin
cb6d819b93 niftyseg: init at 1.0.0 2018-11-16 12:29:29 -05:00
Ben Darwin
6aa3deeb50 niftyreg: init at 1.3.9 2018-11-16 12:24:53 -05:00
Markus J. Ankenbrand
bf05da0967 hmmer: 3.1b2 -> 3.2.1 (#50284) 
This version was released in June 2018 and has many bug fixes
and improvements compared to the previous version from 2015.
See: https://cryptogenomicon.org/2018/06/07/hmmer-3-2-release/
 2018-11-13 15:43:44 +01:00
R. RyanTM
37f01d5bf8 igv: 2.4.14 -> 2.4.15 (#50087) 
Semi-automatic update generated by
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based on information from
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 2018-11-09 22:42:04 -05:00
royneary
bb2bae6986 mosdeph: fix compilation with nim 0.19 2018-10-31 22:03:27 +01:00
R. RyanTM
c759273e2e star: 2.6.1a -> 2.6.1c 
Semi-automatic update generated by
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based on information from
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 2018-10-24 15:22:22 +02:00
R. RyanTM
269efba0aa bowtie2: 2.3.4.2 -> 2.3.4.3 
Semi-automatic update generated by
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based on information from
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 2018-10-03 21:49:10 -07:00
R. RyanTM
77f8e10fed picard-tools: 2.18.12 -> 2.18.14 (#46978) 
Semi-automatic update generated by
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based on information from
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 2018-09-29 21:03:17 +02:00
Orivej Desh
7545b7dcf3 platypus: 2017-03-07 -> 2018-07-22 2018-09-21 22:42:28 +00:00
Orivej Desh
cefd38b721 samtools: 1.8 -> 1.9 2018-09-21 22:42:28 +00:00
Markus J. Ankenbrand
e2df8e7c0f seaview: init at 4.7 (#46595) 2018-09-13 14:10:44 +02:00
R. RyanTM
c4e8db3de0 star: 2.6.0c -> 2.6.1a (#46176) 
Semi-automatic update generated by
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based on information from
star
 2018-09-12 22:49:12 +02:00
Matthew Bauer
40d19d8e7c
Merge pull request #45102 from jbedo/hisat2 
hisat2: init 2.1.0
 2018-09-10 15:11:58 -05:00
R. RyanTM
f72cba212c picard-tools: 2.18.11 -> 2.18.12 
Semi-automatic update generated by
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picard-tools
 2018-09-06 14:22:26 -07:00
xeji
6216f5da04
Merge pull request #45263 from r-ryantm/auto-update/bowtie2 
bowtie2: 2.3.4.1 -> 2.3.4.2
 2018-08-21 19:51:36 +02:00
Uli Baum
c47aafde87 bowtie2: broken on aarch64 
never built as far back as hydra logs go.
 2018-08-21 19:11:37 +02:00
Joachim F
6755ab8b34
Merge pull request #44250 from jbedo/strelka 
strelka: init 2.9.5
 2018-08-20 06:24:15 +00:00
Justin Bedo
27960b6acf
strelka: init 2.9.5 2018-08-20 08:58:22 +10:00
Vladimír Čunát
209730208a
Merge branch 'staging-next' 2018-08-17 20:51:31 +02:00