Commit Graph

409 Commits

Author SHA1 Message Date
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