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Author SHA1 Message Date
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
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 
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 
picard-tools: 2.21.3 -> 2.21.6
 2020-01-22 16:18:57 -08:00
Patrick Hilhorst 593e11fd94
treewide: fix redirected urls 
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) 
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) 
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 
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 
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 
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 
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
Franz Pletz 8e63a6cd13
niftyreg: fix build with gcc9 2019-11-03 14:43:37 +01:00
R. RyanTM 28b0a6a9e0 star: 2.7.2b -> 2.7.3a 2019-11-03 10:23:05 +01:00
Franz Pletz e39773fe5b
megahit: 1.1.4 -> 1.2.9 2019-11-02 15:53:57 +01:00
Ben Darwin ddc2955ad9 EZminc: 2017-08-29 -> 2019-07-25; mark unbroken 2019-10-26 09:55:30 -07:00
scalavision 535a7006ea truvari: init at 1.3.2 (#70877) 
pythonPackages.pyvcf: init at 0.6.8
 2019-10-24 17:06:42 -04:00
R. RyanTM b8acb48b24 picard-tools: 2.20.8 -> 2.21.1 (#71748) 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
 2019-10-23 09:34:40 +02:00
R. RyanTM a9551de99a dcm2niix: 1.0.20190410 -> 1.0.20190902 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/dcm2niix/versions
 2019-10-22 16:31:19 -07:00
Renaud e6f99fa3b1
Merge pull request #69961 from r-ryantm/auto-update/star 
star: 2.7.1a -> 2.7.2b
 2019-10-13 17:10:23 +02:00
scalavision 3d860972ee delly: init at 0.8.1 (#70871) 2019-10-10 22:08:45 -04:00
Linus Heckemann 5aa4b19946 treewide: mark some broken packages as broken 
Refs:
e675498026
1e9cc5b984
793a2fe1e8
c19cf65261
f6544d618f
 2019-10-08 17:14:26 +02:00
Bruno Bzeznik 1ba3f3f00f SPAdes: init at 3.13.1 (#63082) 2019-10-03 09:18:48 +00:00
Ryan Mulligan 8519cd1aa0
Merge pull request #69735 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.20.5 -> 2.20.8
 2019-09-29 15:44:33 -07:00
R. RyanTM de95a92384 star: 2.7.1a -> 2.7.2b 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/star/versions
 2019-09-28 21:09:40 -07:00
R. RyanTM 8c397c2bc2 picard-tools: 2.20.5 -> 2.20.8 
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/picard-tools/versions
 2019-09-27 18:25:22 -07:00
Aaron Andersen af5176b430
Merge pull request #63117 from bzizou/macse 
macse: init at 2.03
 2019-09-27 17:26:07 -04:00
Bruno Bzeznik e4108becbe macse: init at 2.03 2019-09-24 08:24:07 +02:00
Miguel Madrid Mencía 148c82e07e
maintainer: mimadrid: update github username and personal data 2019-09-14 12:15:46 +02:00
Linus Heckemann f6182da2c6 ants: use itk 4.x 2019-09-13 11:54:21 +02:00
volth 7b8fb5c06c treewide: remove redundant quotes 2019-09-08 23:38:31 +00:00
Frederik Rietdijk 5f4734b1dd Merge remote-tracking branch 'upstream/gcc-8' into staging-next 
Earlier the gcc8 branch was merged instead of the gcc-8 branch (note the dash)...
 2019-09-08 20:44:26 +02:00
Frederik Rietdijk 66bc7fc1b3 Merge master into staging-next 2019-09-06 22:46:05 +02:00
Justin Bedo 6beabe7d2c bedtools: 2.28.0 -> 2.29.0 2019-09-06 21:23:15 +02:00
Jan Tojnar cdf426488b
Merge branch 'master' into staging-next 
Fixed trivial conflicts caused by removing rec.
 2019-09-06 03:20:09 +02:00