Markus Kowalewski
6dba41fbcb
mpi: use mpi attribute consistently as the default MPI implementations
...
Use the attribute mpi to provide a system wide default MPI
implementation. The default is openmpi (as before).
This now allows for overriding the MPI implentation by using
the overlay mechanism. Build all packages with mpich instead
of the default openmpi can now be achived like this:
self: super:
{
mpi = super.mpich;
}
All derivations that have been using "mpi ? null" to provide optional
building with MPI have been change in the following way to allow for
optional builds with MPI:
{ ...
, mpi
, useMpi ? false
}
2021-01-23 12:15:13 +01:00
R. RyanTM
e1ea0a237a
picard-tools: 2.24.0 -> 2.24.1
2021-01-22 19:10:27 +00:00
zowoq
932941b79c
treewide: editorconfig fixes
...
- remove trailing whitespace
- use spaces for indentation
2021-01-21 13:29:54 +10:00
R. RyanTM
427bbe059a
picard-tools: 2.23.9 -> 2.24.0
2021-01-20 20:42:01 +00:00
zowoq
759a2cd563
ecopcr: use spaces for indentation
2021-01-20 10:53:10 +10:00
zowoq
31f5dd3f36
treewide: editorconfig fixes
...
- remove trailing whitespace
- use spaces for indentation
2021-01-20 09:11:11 +10:00
Jonathan Ringer
9bb3fccb5b
treewide: pkgs.pkgconfig -> pkgs.pkg-config, move pkgconfig to alias.nix
...
continuation of #109595
pkgconfig was aliased in 2018, however, it remained in
all-packages.nix due to its wide usage. This cleans
up the remaining references to pkgs.pkgsconfig and
moves the entry to aliases.nix.
python3Packages.pkgconfig remained unchanged because
it's the canonical name of the upstream package
on pypi.
2021-01-19 01:16:25 -08:00
Jonathan Ringer
200bb8c977
cd-hit: remove non-existent package
2021-01-19 01:16:25 -08:00
R. RyanTM
a0e1bb6a4b
delly: 0.8.6 -> 0.8.7
2021-01-18 14:22:30 +00:00
Ben Siraphob
badf51221d
treewide: stdenv.lib -> lib
2021-01-16 17:58:11 +07:00
Profpatsch
4a7f99d55d
treewide: with stdenv.lib; in meta -> with lib;
...
Part of: https://github.com/NixOS/nixpkgs/issues/108938
meta = with stdenv.lib;
is a widely used pattern. We want to slowly remove
the `stdenv.lib` indirection and encourage people
to use `lib` directly. Thus let’s start with the meta
field.
This used a rewriting script to mostly automatically
replace all occurances of this pattern, and add the
`lib` argument to the package header if it doesn’t
exist yet.
The script in its current form is available at
https://cs.tvl.fyi/depot@2f807d7f141068d2d60676a89213eaa5353ca6e0/-/blob/users/Profpatsch/nixpkgs-rewriter/default.nix
2021-01-11 10:38:22 +01:00
Jan Tojnar
e6c0c98940
Merge branch 'master' into staging-next
...
zynaddsubfx conflict has been updated to 3.0.1, which conflicted with rewrite after 3.0.5 update on a different branch.
2021-01-08 02:07:34 +01:00
Sandro
7ae17783a7
Merge pull request #108432 from jbedo/fastp
...
fastp: init 0.20.1
2021-01-07 21:44:33 +01:00
Jan Tojnar
f19eb635b4
Merge branch 'master' into staging-next
...
b04fc593e7
2021-01-07 13:04:31 +01:00
Justin Bedo
bdf3d727ca
fastp: init 0.20.1
2021-01-07 18:24:19 +11:00
Sandro
0af4d59732
Merge pull request #108437 from jbedo/varscan
...
varscan: 2.4.2 -> 2.4.4
2021-01-06 00:19:30 +01:00
Sandro
31d6b1cd06
Merge pull request #108435 from jbedo/last
...
last: 1145 -> 1170
2021-01-06 00:18:41 +01:00
Justin Bedo
56dd3fa172
varscan: 2.4.2 -> 2.4.4
2021-01-05 10:55:28 +11:00
Justin Bedo
62432c855f
last: 1145 -> 1170
2021-01-05 10:29:31 +11:00
Sandro Jäckel
a8d360eca3
raxml: cleanup
2021-01-04 11:02:16 +01:00
github-actions[bot]
07165c7226
Merge staging-next into staging
2021-01-03 18:38:32 +00:00
John Ericson
b03fdcc7f9
Merge pull request #108300 from siraben/parallel-cmake
...
treewide: remove enableParallelBuilding = true if using cmake
2021-01-03 13:22:09 -05:00
Pavol Rusnak
77364ac7c0
Merge pull request #108251 from prusnak/bowtie2
...
bowtie2: 2.3.5.1 -> 2.4.2
2021-01-03 13:47:45 +01:00
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
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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
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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
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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
R. RyanTM
ae4d9cb9a0
stacks: 2.52 -> 2.53
2020-05-10 09:37:29 -07:00
R. RyanTM
85b39960b5
SPAdes: 3.14.0 -> 3.14.1
2020-05-10 13:06:19 +00:00
Dmitry Kalinkin
e80302dc7d
Merge pull request #86142 from bcdarwin/itk-5.1.0
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Itk: 5.0.1 -> 5.1.0
2020-05-09 15:03:28 -04:00
Mario Rodas
60762e9524
Merge pull request #86216 from bcdarwin/mrtrix-update
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mrtrix: 3.0_RC3_latest -> 3.0.0
2020-05-07 06:57:44 -05:00
Ben Darwin
6f1430a802
ezminc: switch from itk5 to itk4 branch
...
- itk5 branch currently lacks support for itk 5.1
2020-05-05 00:08:04 -04:00
Mario Rodas
3b6c399fc3
Merge pull request #86720 from r-ryantm/auto-update/picard-tools
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picard-tools: 2.22.2 -> 2.22.4
2020-05-04 06:01:31 -05:00
R. RyanTM
877b1cdad7
picard-tools: 2.22.2 -> 2.22.4
2020-05-04 04:07:44 +00:00
R. RyanTM
d0afae4298
dcm2niix: 1.0.20190902 -> 1.0.20200331
2020-05-02 10:16:22 +02:00
Ben Darwin
70171d321e
mrtrix: 3.0_RC3_latest -> 3.0.0
2020-04-28 10:37:06 -04:00
Lassulus
d0b1de5491
Merge pull request #70401 from bzizou/quast
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Quast: init at 5.0.2
2020-04-24 20:26:04 +02:00
Bruno Bzeznik
db48393552
init at 3.0.0-beta14
2020-04-24 11:20:14 +02:00
Bruno Bzeznik
eb51b462aa
Quast: init at 5.0.2
2020-04-24 10:11:54 +02:00
Justin Bedo
d8d6ecc418
mosdepth: 0.2.6 -> 0.2.9
2020-04-21 19:42:05 +02:00
Matthew Bauer
1c8aba8334
treewide: use blas and lapack
...
This makes packages use lapack and blas, which can wrap different
BLAS/LAPACK implementations.
treewide: cleanup from blas/lapack changes
A few issues in the original treewide:
- can’t assume blas64 is a bool
- unused commented code
2020-04-17 16:24:09 -05:00
Michael Reilly
84cf00f980
treewide: Per RFC45, remove all unquoted URLs
2020-04-10 17:54:53 +01:00
R. RyanTM
92c8881358
picard-tools: 2.22.0 -> 2.22.2
2020-04-01 17:29:55 +00:00
R. RyanTM
3017e6989f
deeptools: 3.3.1 -> 3.4.1
2020-03-30 21:47:32 -07:00
R. RyanTM
bd245a755f
stacks: 2.41 -> 2.52
2020-03-30 16:13:02 -07:00
Ryan Mulligan
c669d2991b
Merge pull request #83464 from r-ryantm/auto-update/last
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last: 1047 -> 1060
2020-03-27 07:34:18 -07:00
R. RyanTM
bd3fbef804
last: 1047 -> 1060
2020-03-27 04:12:41 +00:00
R. RyanTM
4a3ea14b5b
seaview: 5.0 -> 5.0.2
2020-03-26 00:25:29 +00:00
Mario Rodas
5760e001ca
Merge pull request #81706 from r-ryantm/auto-update/picard-tools
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picard-tools: 2.21.8 -> 2.22.0
2020-03-04 07:26:05 -05:00
R. RyanTM
343ec80712
picard-tools: 2.21.8 -> 2.22.0
2020-03-04 09:58:40 +00:00
scalavision
dbb4826457
truvari:1.3.2->1.3.4
2020-03-02 09:15:58 +01:00
Linus Heckemann
0cc83f884a
Merge pull request #80292 from bcdarwin/mrtrix
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mrtrix: init at 3.0_RC3_latest
2020-02-24 13:52:38 +01:00
Ben Darwin
9a2cd20478
mrtrix: init at 3.0_RC3_latest
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This package consists mostly of command-line tools, but there are also two qt5-based image viewers (`mrview` and `shview`). I have provided an option `withGui = true` to allow users to disable these viewers. They work on NixOS but unlikely to work out-of-the box on non-NixOS Linux (see #62169 ), but I've refrained from asserting that they shouldn't be built since a user might want to fiddle with runtime GL stuff.
Some programs rely on FSL and/or ANTs backends; I have somewhat heavy-handedly wrapped all binaries to point to ANTs, while FSL is not available in Nix at the moment and has a non-commercial license so would be convenient to disable by default for Hydra builds.
2020-02-16 22:25:25 -05:00
R. RyanTM
4c6c40d96a
kallisto: 0.46.1 -> 0.46.2
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Co-authored-by: Daniel Schaefer <git@danielschaefer.me>
2020-02-15 22:39:58 +01:00
Dmitry Kalinkin
5f2a3bef33
Merge pull request #79778 from jbedo/delly
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delly: 0.8.1 -> 0.8.2
2020-02-11 03:54:02 -05:00
Justin Bedo
a8fe9e7aff
delly: 0.8.1 -> 0.8.2
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Backported patch required for htslib 1.10.2
2020-02-11 19:21:59 +11:00
Ryan Mulligan
b99e12f4fe
Merge pull request #79534 from r-ryantm/auto-update/last
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last: 1045 -> 1047
2020-02-10 18:10:08 -08:00
Ben Darwin
39f0e3b32b
minc_tools: enable building conversion tools
2020-02-10 19:53:25 +01:00
Ben Darwin
bcad453bcf
minc_tools: 2017-09-11 -> unstable-2019-12-04
2020-02-10 19:53:25 +01:00
R. RyanTM
dae266aa66
last: 1045 -> 1047
2020-02-08 13:04:53 +00:00
R. RyanTM
d5404eebe9
picard-tools: 2.21.6 -> 2.21.8
2020-02-07 17:20:58 +00:00
Frederik Rietdijk
419bc0a4cd
Revert "Revert "Merge master into staging-next""
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In 87a19e9048ac241fb7a50be87c79790be87c7979
2020-02-05 19:41:25 +01:00
Frederik Rietdijk
0be87c7979
Revert "Merge master into staging-next"
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I merged master into staging-next but accidentally pushed it to master.
This should get us back to 87a19e9048ac241fb7a576a439239e
2020-02-05 19:18:35 +01:00
R. RyanTM
3c54ae5679
SPAdes: 3.13.1 -> 3.14.0
2020-02-04 16:40:50 +00:00
R. RyanTM
42fff82421
seaview: 4.7 -> 5.0
2020-01-30 08:26:52 +00:00
Silvan Mosberger
80a2740991
Merge pull request #78265 from Synthetica9/https-homepages
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treewide: fix redirected urls
2020-01-27 15:00:53 +01:00
Justin Bedo
7f142260d3
manta: init 1.6.0
2020-01-24 02:02:19 -08:00
Ryan Mulligan
a6dc361cae
Merge pull request #78261 from r-ryantm/auto-update/picard-tools
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picard-tools: 2.21.3 -> 2.21.6
2020-01-22 16:18:57 -08:00
Patrick Hilhorst
593e11fd94
treewide: fix redirected urls
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According to https://repology.org/repository/nix_unstable/problems , we have a
lot of packages that have http links that redirect to https as their homepage.
This commit updates all these packages to use the https links as their
homepage.
The following script was used to make these updates:
```
curl https://repology.org/api/v1/repository/nix_unstable/problems \
| jq '.[] | .problem' -r \
| rg 'Homepage link "(.+)" is a permanent redirect to "(.+)" and should be updated' --replace 's@$1@$2@' \
| sort | uniq > script.sed
find -name '*.nix' | xargs -P4 -- sed -f script.sed -i
```
2020-01-22 11:26:22 +01:00
R. RyanTM
fff7a7a862
picard-tools: 2.21.3 -> 2.21.6
2020-01-22 10:12:28 +00:00
Jonathan Ringer
4de137a77d
samtools: 1.9 -> 1.10
2020-01-19 13:13:01 -08:00
Jonathan Ringer
5961f211f3
python.pkgs wide: fix problematic urls
2020-01-10 21:02:12 -08:00
Bruno Bzeznik
f7a4e4a93a
bayescan: init at 2.1 ( #68191 )
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Co-authored-by: Dmitry Kalinkin <dmitry.kalinkin@gmail.com>
2020-01-09 12:38:53 -05:00
Luis Pedro Coelho
fdfebafc10
blast: init at 2.10.0 ( #61430 )
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Co-authored-by: Pavel Chuprikov <pschuprikov@gmail.com>
2020-01-07 20:14:18 +01:00
R. RyanTM
4bc4c70bc6
last: 1042 -> 1045
2020-01-06 11:46:28 -08:00
Frederik Rietdijk
7aa2b0215b
Merge master into staging-next
2020-01-03 10:25:14 +01:00
Ryan Mulligan
ec29bb50bf
Merge pull request #76208 from r-ryantm/auto-update/bcftools
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bcftools: 1.9 -> 1.10.2
2020-01-02 16:42:27 -08:00
Frederik Rietdijk
6d059becd3
Merge gcc-9 into staging ( #68029 )
2019-12-30 16:38:38 +01:00
Merijn Broeren
133103d709
treewide: replace make/build/configure/patchFlags with nix lists
2019-12-30 12:58:11 +01:00
Franz Pletz
a88fc6be6d
strelka: fix build w/ gcc9
2019-12-30 03:18:19 +01:00
Frederik Rietdijk
eda01862c4
Merge pull request #75900 from jbedo/tebreak
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Tebreak, minia, last, bx-python, python-lzo
2019-12-29 10:24:31 +01:00
Justin Bedo
11460d4cac
tebreak: init at 1.0
2019-12-29 17:16:10 +11:00
Franz Pletz
77b6c3cd06
Merge remote-tracking branch 'origin/master' into gcc-9
2019-12-26 14:17:36 +01:00
R. RyanTM
c905a6da5a
bcftools: 1.9 -> 1.10.2
2019-12-22 20:00:29 -08:00
Justin Bedo
2191912274
minia: init at 3.2.1
2019-12-20 11:27:04 +11:00
Justin Bedo
6741cff527
last: init at 1042
2019-12-20 11:27:02 +11:00
Justin Bedo
28a057a56b
bedtools: 2.29.1 -> 2.29.2
2019-12-18 10:39:25 +11:00
Mario Rodas
5e5ce79db4
Merge pull request #75807 from jbedo/strelka
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strelka: fix broken build
2019-12-16 23:52:35 -05:00
Justin Bedo
c3f09c33eb
strelka: fix broken build
2019-12-17 11:20:32 +11:00
Justin Bedo
50fbca4bfc
bedtools: fix clang builds
2019-12-11 09:27:57 +11:00
Justin Bedo
592d288aa2
bedtools: 2.29.0 -> 2.29.1
2019-12-10 13:24:27 +11:00
Renato Alves
e18fb092f1
kssd: init at 1.0
2019-12-08 16:48:59 +01:00
scalavision
3dfabd6eff
svaba: init at 1.1.0
2019-12-08 14:51:05 +01:00
Mario Rodas
835705d11b
Merge pull request #75095 from tbenst/bftools
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bftools: 5.9.2 -> 6.3.0
2019-12-07 03:06:00 -05:00
Tyler Benster
2700559bdc
bftools: 5.9.2 -> 6.3.0
2019-12-06 02:11:00 -08:00
R. RyanTM
605e88517b
paml: 4.9i -> 4.9j
2019-12-01 18:43:58 +01:00
R. RyanTM
da09e1e772
kallisto: 0.46.0 -> 0.46.1 ( #74430 )
2019-11-30 21:12:54 +01:00
R. RyanTM
98e0ead3ba
picard-tools: 2.21.1 -> 2.21.3 ( #74528 )
2019-11-30 16:24:44 +01:00
R. RyanTM
6563dd3351
hmmer: 3.2.1 -> 3.3
2019-11-27 18:40:23 -08:00
Kai Wohlfahrt
6b2504f9f2
freebayes: 2017-08-23 -> 1.3.1 (2019-06-03)
2019-11-20 09:10:31 -08:00
Ben Darwin
736860d34b
nifticlib and niftseg: change platform from linux to unix since these build on OSX
2019-11-14 21:25:10 -05:00
Franz Pletz
8dca8b9ccb
Merge remote-tracking branch 'origin/master' into gcc-9
2019-11-05 01:07:22 +01:00
scalavision
d9b40f6397
deeptools: init at 3.3.1
2019-11-04 02:42:36 -08:00
Franz Pletz
6b10b78872
Merge remote-tracking branch 'origin/master' into gcc-9
2019-11-03 14:44:12 +01:00
