zowoq
932941b79c
treewide: editorconfig fixes
...
- remove trailing whitespace
- use spaces for indentation
2021-01-21 13:29:54 +10:00
R. RyanTM
427bbe059a
picard-tools: 2.23.9 -> 2.24.0
2021-01-20 20:42:01 +00:00
zowoq
759a2cd563
ecopcr: use spaces for indentation
2021-01-20 10:53:10 +10:00
zowoq
31f5dd3f36
treewide: editorconfig fixes
...
- remove trailing whitespace
- use spaces for indentation
2021-01-20 09:11:11 +10:00
Jonathan Ringer
9bb3fccb5b
treewide: pkgs.pkgconfig -> pkgs.pkg-config, move pkgconfig to alias.nix
...
continuation of #109595
pkgconfig was aliased in 2018, however, it remained in
all-packages.nix due to its wide usage. This cleans
up the remaining references to pkgs.pkgsconfig and
moves the entry to aliases.nix.
python3Packages.pkgconfig remained unchanged because
it's the canonical name of the upstream package
on pypi.
2021-01-19 01:16:25 -08:00
Jonathan Ringer
200bb8c977
cd-hit: remove non-existent package
2021-01-19 01:16:25 -08:00
R. RyanTM
a0e1bb6a4b
delly: 0.8.6 -> 0.8.7
2021-01-18 14:22:30 +00:00
Ben Siraphob
badf51221d
treewide: stdenv.lib -> lib
2021-01-16 17:58:11 +07:00
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
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
