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513 commits

Author SHA1 Message Date
Ryan Mulligan 4ce30eb63a
Merge pull request #105672 from r-ryantm/auto-update/hmmer 
hmmer: 3.3.1 -> 3.3.2
 2020-12-02 05:45:57 -08:00
R. RyanTM 6f50c5b18e hmmer: 3.3.1 -> 3.3.2 2020-12-02 09:00:15 +00:00
Ben Darwin ee7d83e648 ants: unbreak on Darwin 2020-12-01 14:17:54 -05:00
Justin Bedo 5fc6258043
bwa: expand supported platforms 2020-11-30 09:46:51 +11:00
R. RyanTM 212ba486d6 igv: 2.8.12 -> 2.8.13 2020-11-28 02:18:00 +00:00
Sandro c2d728f195
Merge pull request #102140 from SuperSandro2000/patch-2 2020-11-26 01:00:22 +01:00
Sandro d8b570e6c8
Merge pull request #98363 from jbedo/mosdepth 
mosdepth: 0.2.9 -> 0.3.1
 2020-11-25 23:55:47 +01:00
Sandro e166f22759
tebreak: Fix tests 2020-11-25 21:36:38 +01:00
Sandro 5f2997686c
deeptools: Fix tests 2020-11-25 21:36:37 +01:00
R. RyanTM 3b17793827 star: 2.7.5c -> 2.7.6a 2020-11-23 20:40:05 +01:00
Ryan Mulligan 80b6df2a17
Merge pull request #103525 from r-ryantm/auto-update/samblaster 
samblaster: 0.1.24 -> 0.1.26
 2020-11-16 19:03:03 -08:00
Ryan Mulligan 47fe890182
Merge pull request #103751 from r-ryantm/auto-update/last 
last: 1133 -> 1145
 2020-11-14 15:08:46 -08:00
R. RyanTM a698dfa0a2 last: 1133 -> 1145 2020-11-13 23:30:53 +00:00
R. RyanTM 82d1113013 igv: 2.8.11 -> 2.8.12 2020-11-13 18:25:51 +00:00
R. RyanTM d1baaef83d samblaster: 0.1.24 -> 0.1.26 2020-11-12 01:43:02 +00:00
Ryan Mulligan ba3fc8bf47
Merge pull request #102707 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.23.4 -> 2.23.8
 2020-11-04 06:11:08 -08:00
R. RyanTM 6391d3c1b5 picard-tools: 2.23.4 -> 2.23.8 2020-11-04 04:53:50 +00:00
Kevin Cox d7a0daf2a1
Merge pull request #102420 from freezeboy/remove-plink 
plink: remove (broken since 2014)
 2020-11-03 07:49:09 -05:00
R. RyanTM 8ef46be2a4 igv: 2.8.9 -> 2.8.11 2020-11-02 10:16:32 +00:00
freezeboy 1f7e201e9e plink: remove (broken since 2014) 2020-11-02 03:24:16 +01:00
Justin Bedo 32573f4b6e
last: 1066 -> 1133 2020-10-31 10:59:02 +11:00
Renato Alves 6e19ed0a52
lumpy: 0.3.0 -> 0.3.1 2020-10-30 01:28:00 +01:00
Renato Alves a28e5b0a4f
samtools: 1.10 -> 1.11 2020-10-29 18:27:22 +01:00
Ben Siraphob db74029e3e treewide: remove package names from prefix of descriptions 2020-10-27 09:15:07 -07:00
Ben Siraphob 683a87dbeb treewide: remove periods from end of package descriptions 2020-10-17 08:22:31 -07:00
Ryan Mulligan f9728adae7
Merge pull request #99128 from jbedo/delly 
delly: 0.8.2 -> 0.8.5
 2020-10-16 06:30:11 -07:00
R. RyanTM a3dca9576b deeptools: 3.4.1 -> 3.5.0 2020-10-16 00:42:47 -07:00
Doron Behar 1db3202722
Merge pull request #75843 from jbedo/lumpy 2020-10-15 19:46:13 +03:00
Ben Darwin e673c285e1 conglomerate: update LIBMINC_DIR to reflect libminc CMake changes 2020-10-06 15:31:18 -04:00
Ben Darwin 44f2bf87d6 EZminc: update LIBMINC_DIR to reflect libminc CMake changes 2020-10-06 15:31:18 -04:00
Ben Darwin 83d0571ae6 mni_autoreg: update LIBMINC_DIR due to CMake changes in libminc 2020-10-06 15:31:17 -04:00
Ben Darwin 9a190786a4 n3: 2017-09-18 -> 2018-08-09 
- update LIBMINC_DIR and EBTKS_DIR due to CMake updates in those packages
 2020-10-06 15:31:16 -04:00
Ben Darwin 7772e248ab inormalize: update LIBMINC_DIR and dependencies due to libminc update 2020-10-06 15:31:16 -04:00
Ben Darwin 91a429a148 minc_tools: unstable-2019-12-04 -> unstable-2020-07-25 2020-10-06 15:31:14 -04:00
Justin Bedo d8d8f9390a
delly: 0.8.2 -> 0.8.5 2020-10-01 18:09:53 +10:00
Justin Bedo 634927a402
mosdepth: 0.2.9 -> 0.3.1 2020-09-30 09:48:47 +10:00
Robert Scott 8db3ea1ef1
Merge pull request #98614 from r-burns/aragorn 
aragorn: fix build on darwin
 2020-09-25 19:58:10 +01:00
Ryan Burns 6cc2d3e6f2 aragorn: fix build on darwin 
Use environment-specified $CC for C compiler
 2020-09-23 20:45:21 -07:00
Ryan Mulligan dfd2eeabd6
Merge pull request #69644 from bzizou/obitools 
obitools3: init at 3.0.0-beta14
 2020-09-23 19:04:11 -07:00
Daniël de Kok af5b1a9f94
Merge pull request #98427 from jbedo/octopus 
octopus-caller: 0.6.3 -> 0.7.0
 2020-09-23 08:24:10 +02:00
Justin Bedo 4bbdb75f22
octopus-caller: 0.6.3 -> 0.7.0 2020-09-22 08:43:04 +10:00
Robert Scott ecd5886830 truvari: 1.3.4 -> 2.0.2, fixing build 
seeing it has no tests, use pythonImportsCheck in an attempt to detect
total breakage, even though it's not intended to be used as an importable
module
 2020-09-20 12:25:17 +01:00
Robert Scott f1d2491057 bwa: include static library and some key headers in output 2020-09-20 12:23:18 +01:00
Robert Scott 4637721bc1 truvari: fix build 
be less strict about versions
 2020-09-19 20:25:08 -07:00
Emery Hemingway dc09e3edfc nim: wrap compiler for cross-compilation support 2020-09-07 16:16:55 +02:00
Emery Hemingway 06ac3c1d2a nim: patch to fix dynamic library loading 2020-09-07 16:16:55 +02:00
Vladimír Čunát 0ecc8b9a56
Merge #97229: picard-tools: 2.23.3 -> 2.23.4 2020-09-07 09:38:34 +02:00
R. RyanTM cc797c4ab8 star: 2.7.4a -> 2.7.5c 2020-09-05 18:44:51 +00:00
R. RyanTM 1c368b0f13 picard-tools: 2.23.3 -> 2.23.4 2020-09-05 14:02:32 +00:00
Silvan Mosberger cf47ba66fb
Merge pull request #81129 from scalavision/igv-update-28x 
igv: 2.4.19 -> 2.8.0
 2020-08-23 19:24:33 +02:00