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
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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
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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
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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
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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
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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
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- 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
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- 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
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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
