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Author SHA1 Message Date
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 seems to have accidentally changed mkDerivation function for dfilemanager and solarus-quest-editor so I have reverted that here.
 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 
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
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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 
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"" 
In 87a19e9048 I merged staging-next into master using the GitHub gui as intended.
In ac241fb7a5 I merged master into staging-next for the next staging cycle, however, I accidentally pushed it to master.
Thinking this may cause trouble, I reverted it in 0be87c7979. This was however wrong, as it "removed" master.

This reverts commit 0be87c7979.
 2020-02-05 19:41:25 +01:00
Frederik Rietdijk 0be87c7979 Revert "Merge master into staging-next" 
I merged master into staging-next but accidentally pushed it to master.
This should get us back to 87a19e9048.

This reverts commit ac241fb7a5, reversing
changes made to 76a439239e.
 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