github-actions[bot]
0649757570
Merge staging-next into staging
2021-01-03 12:24:59 +00:00
Ben Siraphob
3ae5e6ce03
treewide: remove enableParallelBuilding = true if using cmake
2021-01-03 18:37:40 +07:00
Pavol Rusnak
9139eb5aee
bowtie2: 2.3.5.1 -> 2.4.2
2021-01-02 22:18:32 +01:00
Pavol Rusnak
03b99f0721
bowtie: init at at 1.3.0
2021-01-02 19:46:59 +01:00
Ben Siraphob
b04fc593e7
treewide: cmake buildInputs to nativeBuildInputs, minor cleanups
2021-01-01 11:52:33 +07:00
Justin Bedo
3a65e29d4b
SPAdes: add python dependency
2020-12-21 08:29:57 +11:00
Mario Rodas
7666fb25d0
Merge pull request #106856 from jbedo/delly
...
delly: 0.8.5 -> 0.8.6
2020-12-14 08:10:03 -05:00
Justin Bedo
6ce06dccfc
delly: 0.8.5 -> 0.8.6
2020-12-14 09:55:57 +11:00
R. RyanTM
aa2148eb1f
picard-tools: 2.23.8 -> 2.23.9
2020-12-10 23:06:36 +00:00
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
scalavision
78e89143d4
igv: 2.4.19 -> 2.8.9
...
Co-Authored-By: Silvan Mosberger <contact@infinisil.com>
2020-08-23 19:23:04 +02:00
Lassulus
7623640e54
Merge pull request #89868 from r-ryantm/auto-update/star
...
star: 2.7.3a -> 2.7.4a
2020-08-22 13:35:13 +02:00
Lassulus
de25713886
Merge pull request #91647 from jbedo/whisper
...
whisper: init at 2.0.1
2020-08-21 18:09:35 +02:00
Justin Bedo
20c8945467
hisat2: 2.1.0 -> 2.2.1
2020-08-16 13:30:53 +00:00
R. RyanTM
afb809f30b
kssd: 1.0 -> 1.1
2020-08-14 15:06:11 +00:00
R. RyanTM
44181da7b7
picard-tools: 2.23.1 -> 2.23.3
2020-08-02 10:04:36 +00:00
Mario Rodas
552a1f9278
itsx: enable on darwin
2020-07-28 13:48:55 -05:00
Mario Rodas
b7c9ca336f
hmmer: enable on darwin
2020-07-28 13:47:34 -05:00
R. RyanTM
58e7ed9d56
hmmer: 3.3 -> 3.3.1
2020-07-28 16:39:23 +00:00
Daniël de Kok
56c841393a
sortmerna: 3.0.3 -> 4.2.0
...
- Fixes build against rocksdb 6.10.2
- Use dynamic rocksdb and zlib libraries
- Build a dynamic binary
2020-07-18 18:06:23 +02:00
Ryan Mulligan
891e3cb973
Merge pull request #92575 from r-ryantm/auto-update/seaview
...
seaview: 5.0.2 -> 5.0.4
2020-07-15 21:23:13 -07:00
R. RyanTM
e6113be804
seaview: 5.0.2 -> 5.0.4
2020-07-07 13:30:35 +00:00
Benjamin Hipple
0f94e2413d
Merge pull request #91071 from bcdarwin/minc-tools-build-nifti-tools
...
minc-tools: actually build Nifti support
2020-07-06 17:45:48 -04:00
Ben Darwin
28becad9be
minc-tools: actually build Nifti support
2020-07-06 11:09:33 -04:00
Justin Bedo
3139597277
whisper: init at 2.0.1
2020-07-06 18:59:45 +10:00
R. RyanTM
aca998de5e
last: 1061 -> 1066
2020-07-05 08:43:25 +00:00
Justin Bedo
a3d6e7b4b4
lumpy: init 0.3.0
2020-07-05 09:19:11 +10:00
Justin Bedo
617483d27a
sambamba: init 0.7.1
2020-07-05 09:10:21 +10:00
Justin Bedo
2ada3b5d3e
samblaster: init 0.1.24
2020-07-05 09:10:21 +10:00
Mario Rodas
c70f0c6548
Merge pull request #92257 from r-ryantm/auto-update/tebreak
...
tebreak: 1.0 -> 1.1
2020-07-04 12:45:00 -05:00
R. RyanTM
d8956ba50e
tebreak: 1.0 -> 1.1
2020-07-04 10:45:49 +00:00
R. RyanTM
6630edb1bd
picard-tools: 2.23.0 -> 2.23.1
2020-07-02 18:09:49 -07:00
Markus Kowalewski
c317091b5a
mrbayes: fix license
2020-06-26 11:06:35 +02:00
Markus Kowalewski
83dda57082
emboss: fix license
2020-06-26 11:05:24 +02:00
Mario Rodas
c89c819abd
Merge pull request #98672 from r-ryantm/auto-update/bcftools
...
bcftools: 1.10.2 -> 1.11
2020-10-02 23:57:06 -05:00
Ryan Mulligan
6aadae67de
Merge pull request #81550 from scalavision/add-kent-utils-to-bioinf
...
kent: init at 394
2020-10-02 09:05:51 -07:00
Scalavision
a6f124f57b
kent: init at 404
2020-10-01 19:50:37 +02:00
Ben Darwin
a94d0fe675
mrtrix: 3.0.0 -> 3.0.2
2020-09-30 22:13:18 -04:00
R. RyanTM
f4d3204486
bcftools: 1.10.2 -> 1.11
2020-09-24 18:53:07 +00:00
R. RyanTM
57a49ce3a4
picard-tools: 2.22.9 -> 2.23.0
2020-06-15 00:57:30 +00:00
R. RyanTM
b1049a61f1
star: 2.7.3a -> 2.7.4a
2020-06-09 02:32:13 +00:00
R. RyanTM
170ea57065
picard-tools: 2.22.8 -> 2.22.9
2020-06-06 15:43:25 +00:00
Benjamin Hipple
f04a5af0cc
Merge pull request #82180 from bcdarwin/bppcore
...
bppsuite: init at 2.4.1
2020-05-26 21:07:25 -04:00
Benjamin Hipple
d3082a31cd
Merge pull request #87544 from bcdarwin/vtk-8
...
vtk: 7.1.1 -> 8.2.0
2020-05-26 00:24:28 -04:00
Ben Darwin
45cd7beeb2
bppsuite: init at 2.4.1
2020-05-25 21:13:02 -04:00
R. RyanTM
a60a040236
picard-tools: 2.22.7 -> 2.22.8
2020-05-25 01:25:17 +00:00
Ryan Mulligan
5505be7840
Merge pull request #88568 from r-ryantm/auto-update/last
...
last: 1060 -> 1061
2020-05-23 11:42:47 -07:00
R. RyanTM
25841d95c5
last: 1060 -> 1061
2020-05-22 02:21:55 +00:00
R. RyanTM
3450729658
picard-tools: 2.22.4 -> 2.22.7
2020-05-19 21:56:38 +00:00
Ryan Mulligan
fdf4439acc
Merge pull request #87494 from r-ryantm/auto-update/SPAdes
...
SPAdes: 3.14.0 -> 3.14.1
2020-05-18 08:06:19 -07:00
Ben Darwin
5e716bf469
vtk: 7.1.1 -> 8.2.0
...
- also create vtk_7 as several packages don't build with 8.x:
- itk5: vtkVersion.h header not found at compile time
- ants: version in tree (2.2.0) is incompatible with 8.2
- itk4: ants depends on both vtk and itk4, so use vtk_7
- gdcm: vtk header issue
- python3Packages.vtk: Python C API compilation error with Python 3.8
- upgrade vtkWithQt4 -> vtkWithQt5
2020-05-11 17:54:29 -04:00