Commit graph

592 commits

Author SHA1 Message Date
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:
e6754980264fe927320d5ff2dbd24ca4fac9a160
1e9cc5b9844ef603fe160e9f671178f96200774f
793a2fe1e8bb886ca2096c5904e1193dc3268b6d
c19cf65261639f749012454932a532aa7c681e4b
f6544d618f30fae0bc4798c4387a8c7c9c047a7c
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
Justin Bedo 3f83cbf538
xenomapper: init 1.0.2 2019-09-05 20:50:22 +10:00
Franz Pletz de85797565
Merge remote-tracking branch 'origin/master' into gcc-8 2019-09-03 22:15:07 +02:00
Vladimír Čunát f21211ebfe
Merge branch 'master' into staging 2019-09-02 23:25:24 +02:00
Tadeo Kondrak 2aa9b655f4
kallisto: 0.43.1 -> 0.46.0 2019-08-31 14:06:31 -06:00
Frederik Rietdijk 98ef78326d Merge staging-next into staging 2019-08-31 18:07:33 +02:00
Frederik Rietdijk 96e5474329 Merge master into staging-next 2019-08-31 18:04:31 +02:00
Lassulus a8d26fc34a
Merge pull request #63127 from bzizou/trimal
trimal: init at 1.4.1
2019-08-31 13:04:41 +02:00
Frederik Rietdijk ad1d58c622 Merge staging-next into staging 2019-08-31 10:04:20 +02:00
Frederik Rietdijk fc74ba8291 Merge master into staging-next 2019-08-31 09:50:38 +02:00
volth 08f68313a4 treewide: remove redundant rec 2019-08-28 11:07:32 +00:00
Léo Gaspard 8a4721d606
Merge pull request #64669 from luispedro/add_sortmerna
sortmerna: init at 3.0.3
2019-08-27 17:19:53 +02:00
Luis Pedro Coelho bc22c2e07f sortmerna: init at 3.0.3
This is a useful package in bioinformatics, namely in processing
short-read sequencing data from metagenomes
2019-08-27 00:37:43 +02:00
Robin Gloster 616b8343c4
Merge remote-tracking branch 'upstream/master' into gcc-8 2019-08-25 18:55:46 +02:00
Vladimír Čunát 2e6bf42a22
Merge branch 'master' into staging-next
There ver very many conflicts, basically all due to
name -> pname+version.  Fortunately, almost everything was auto-resolved
by kdiff3, and for now I just fixed up a couple evaluation problems,
as verified by the tarball job.  There might be some fallback to these
conflicts, but I believe it should be minimal.

Hydra nixpkgs: ?compare=1538299
2019-08-24 08:55:37 +02:00
R. RyanTM 41571dc81a picard-tools: 2.20.4 -> 2.20.5
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
2019-08-19 21:40:40 -07:00
volth 46420bbaa3 treewide: name -> pname (easy cases) (#66585)
treewide replacement of

stdenv.mkDerivation rec {
  name = "*-${version}";
  version = "*";

to pname
2019-08-15 13:41:18 +01:00
R. RyanTM 3bfd09b76d picard-tools: 2.20.3 -> 2.20.4
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
2019-08-04 23:04:42 -07:00
Robin Gloster c6f1c9044b
Merge pull request #63282 from jbedo/strelka
strelka: 2.9.5 -> 2.9.10
2019-08-01 23:44:58 +00:00
lewo 481bb449a2
Merge pull request #64897 from bzizou/est-sfs
est-sfs: init at 2.03
2019-07-22 22:52:16 +02:00
Justin Bedo 11ed86d873 bedtools: 2.27.1 -> 2.28.0 2019-07-20 14:15:38 +02:00
R. RyanTM 9a6f0ca8b7 stacks: 2.4 -> 2.41
Semi-automatic update generated by
https://github.com/ryantm/nixpkgs-update tools. This update was made
based on information from
https://repology.org/metapackage/stacks/versions
2019-07-17 09:34:10 +02:00
Ryan Mulligan e7920cbcfc
Merge pull request #64862 from r-ryantm/auto-update/picard-tools
picard-tools: 2.20.2 -> 2.20.3
2019-07-16 20:04:43 -07:00
Bruno Bzeznik 9a22c8c697 est-sfs: init at 2.03 2019-07-16 13:55:59 +02:00
R. RyanTM b7fc14d8e6 picard-tools: 2.20.2 -> 2.20.3
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
2019-07-15 21:46:51 -07:00
worldofpeace 7ce0cc0a6a
Merge pull request #64324 from jbedo/hisat2
hisat2: fix missing perl dependency
2019-07-13 13:21:11 -04:00
Ryan Mulligan 508ae42a0f treewide: fix redirect URLs 2019-07-10 12:52:51 -07:00
Justin Bedo d2d449cea5
hisat2: fix missing perl dependency 2019-07-05 10:29:51 +10:00
markuskowa a07d045b00
Merge pull request #63488 from jbedo/octopus
octopus: init 0.6.3-beta
2019-06-27 12:43:25 +02:00
royneary d162165350
mosdepth: 0.2.3 -> 0.2.6 2019-06-22 22:41:59 +02:00
Justin Bedo b8b71aaaf9
octopus: init 0.6.3-beta 2019-06-19 23:09:33 +10:00
Linus Heckemann 2458209c3e dcm2niix: 1.0.20170130 -> 1.0.20190410 2019-06-18 22:12:40 +02:00
Justin Bedo 1be8ba08d3
strelka: 2.9.5 -> 2.9.10 2019-06-17 16:09:25 +10:00
Franz Pletz 394bee72db
ants: fix build with gcc8 2019-06-17 07:26:00 +02:00
volth f3282c8d1e treewide: remove unused variables (#63177)
* treewide: remove unused variables

* making ofborg happy
2019-06-16 19:59:05 +00:00
Bruno Bzeznik aafffb2614 trimal: init at 1.4.1 2019-06-14 16:31:39 +02:00
Aaron Andersen 4cb64dba39
Merge pull request #58362 from bzizou/cd-hit
cd-hit: init at 4.8.1
2019-06-13 20:39:54 -04:00
Bruno Bzeznik 9fbf8625f1 cd-hit: init at 4.8.1 2019-06-13 14:35:13 +02:00
Robert Scott 48c8756157 pythonPackages.neuron: restrict to x86 platforms 2019-06-09 12:18:58 +02:00
Robert Scott e0aec554eb pythonPackages.neuron: fix for darwin
un-compensate for some of the darwin quirks the neuron
source is expecting
2019-06-09 12:18:58 +02:00
R. RyanTM 8ebf0eefbe star: 2.7.0f -> 2.7.1a (#62577)
* star: 2.7.0f -> 2.7.1a

Semi-automatic update generated by
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* star: cleanup
2019-06-06 18:10:34 +02:00
Matthew Bauer d598eca41e
Merge pull request #62752 from matthewbauer/darwin-fixes100
Fixes for x86_64-darwin failures on Hydra
2019-06-06 09:46:41 -04:00
Matthew Bauer 441485af66 iv: only use patchelf on linux 2019-06-05 23:42:58 -04:00
R. RyanTM 2998ac28b4 picard-tools: 2.19.2 -> 2.20.2
Semi-automatic update generated by
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2019-06-02 05:31:59 -07:00
Ryan Mulligan 34e8f3b119
Merge pull request #61997 from r-ryantm/auto-update/stacks
stacks: 2.3e -> 2.4
2019-05-24 06:31:43 -07:00
R. RyanTM f4a20199d2 stacks: 2.3e -> 2.4
Semi-automatic update generated by
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based on information from
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2019-05-24 03:50:06 -07:00
Robin Gloster 43aa2e30c3
Merge pull request #58369 from bzizou/clustalo
clustal-omega: init at 1.2.4
2019-05-18 10:16:43 +00:00
Renaud bf4728cb40
eggnog-mapper: fix patch URL and hash 2019-05-13 16:00:07 +02:00
R. RyanTM ad5676f8b9 minimap2: 2.16 -> 2.17
Semi-automatic update generated by
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2019-05-11 21:12:42 -07:00
Frederik Rietdijk 155c9d8e18 Merge master into staging-next 2019-05-02 08:43:14 +02:00
R. RyanTM d41da19c65 picard-tools: 2.19.0 -> 2.19.2
Semi-automatic update generated by
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2019-05-01 17:49:08 -07:00
Frederik Rietdijk f137783927 Merge master into staging-next 2019-05-01 11:45:46 +02:00
R. RyanTM cc82f81d9a bowtie2: 2.3.5 -> 2.3.5.1
Semi-automatic update generated by
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2019-05-01 11:17:16 +02:00
Matthew Bauer a3990c9f6d
Merge pull request #60447 from matthewbauer/macos-10-12-fixups
Fixup from macos-10-12 branch
2019-04-30 10:06:45 -04:00
Frederik Rietdijk 3462fe27d9 Merge staging-next into staging 2019-04-30 15:52:19 +02:00
Matthew Bauer 74c784a79c treewide: make -Wno-error flags clang-only
In 724e833ea2, I was a little too aggressive in enabling these flags.
Many don’t work in gcc, and we should probably avoid settings them
widely. This makes those flags optional on isclang
2019-04-29 21:34:24 -04:00
Bruno Bzeznik 83886b3d91 aragorn: init at 1.2.38 (#58354) 2019-04-29 07:18:03 -04:00
Matthew Bauer 87944c3125
Merge pull request #56744 from matthewbauer/macos-10-12
Update macOS to 10.12
2019-04-26 22:20:03 -04:00
Matthew Bauer 724e833ea2 treewide: disable -Werror for llvm 7
Some of these have errors on newest llvm. It’s easiest to just add
-Wno-error in these cases.
2019-04-26 21:55:04 -04:00
Renaud 71c6157fd7
Merge pull request #58534 from bzizou/sumatools.dev
sumatools: init at 1.0.34
2019-04-24 22:34:35 +02:00
R. RyanTM 0dc3184871 picard-tools: 2.18.27 -> 2.19.0 (#59634)
Semi-automatic update generated by
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2019-04-20 13:15:40 +02:00
Aaron Andersen 11cf1a282d
Merge pull request #58377 from bzizou/exonerate
exonerate: init at 2.4.0
2019-04-19 13:25:49 -04:00
Bruno Bzeznik 6a8c9bff8f exonerate: init at 2.4.0 2019-04-19 14:58:57 +02:00
Bruno Bzeznik 90b4796c60 sumatools: init at 1.0.34 2019-04-19 14:43:40 +02:00
Luis Pedro Coelho 3fc55eec05 Prodigal: init at 2.6.3 2019-04-19 08:38:14 +02:00
R. RyanTM d11731130d star: 2.7.0c -> 2.7.0f
Semi-automatic update generated by
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2019-04-16 18:30:49 +02:00
Luis Pedro Coelho 13a1f2c296 eggnog-mapper: init at 1.0.3 (#58905) 2019-04-14 17:22:47 -07:00
Frederik Rietdijk 4a125f6b20 Merge master into staging-next 2019-04-07 08:33:41 +02:00
Pascal Wittmann cfb6ade58c
Merge pull request #58931 from bzizou/migrate
migrate: init at 3.7.2
2019-04-06 14:23:50 +02:00
Jan Tojnar cb1a20499a
Merge branch 'master' into staging 2019-04-05 11:37:15 +02:00
Bruno Bzeznik 0b03f44c2f migrate: init at 3.7.2 2019-04-05 09:01:36 +02:00
markuskowa 126e1f8fd0
Merge pull request #58538 from bzizou/stacks
stacks: init at 2.3e
2019-04-03 14:41:00 +02:00
Bruno Bzeznik e7899d2a00 stacks: init at 2.3e 2019-04-03 14:01:32 +02:00
John Ericson 4ccb74011f Merge commit '18aa59b0f26fc707e7313f8467e67159e61600c2' from master into staging
There was one conflict in the NixOS manual; I checked that it still
built after resolving it.
2019-04-01 00:40:03 -04:00
markuskowa c637aeff19
Merge pull request #58541 from luispedro/add_megahit
megahit: init at 1.1.4
2019-03-31 12:51:59 +02:00
Luis Pedro Coelho bf48451959 megahit: init at 1.1.4
This is widely used in bioinformatics for assembling genomes &
metagenomes
2019-03-31 05:56:14 +02:00
R. RyanTM 893abe12e8 bowtie2: 2.3.4.3 -> 2.3.5 (#58014)
Semi-automatic update generated by
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2019-03-31 00:37:38 +01:00
R. RyanTM 2ce544a8b1 minimap2: 2.15 -> 2.16 (#57319)
Semi-automatic update generated by
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2019-03-27 23:25:52 +01:00
R. RyanTM 1b73fd1954 paml: 4.9h -> 4.9i (#57354)
Semi-automatic update generated by
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2019-03-27 15:44:21 +01:00
Bruno Bzeznik 00431493c0 itsx: init at 1.1.1 2019-03-26 15:52:35 +01:00
Bruno Bzeznik 6858d0fd62 clustal-omega: init at 1.2.4 2019-03-26 15:45:59 +01:00