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557 commits

Author SHA1 Message Date
Mario Rodas f9a095da28
Merge pull request #112191 from r-ryantm/auto-update/star 
star: 2.7.6a -> 2.7.7a
 2021-02-08 20:17:49 -05:00
Ryan Mulligan 64c446d0ba
Merge pull request #112021 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.24.1 -> 2.24.2
 2021-02-07 14:57:32 -08:00
R. RyanTM ef6ed50cb4 star: 2.7.6a -> 2.7.7a 2021-02-06 19:50:22 +00:00
Orivej Desh 8d0af26e1d blast: 2.10.0 -> 2.11.0 
Fixes build with gcc10.
 2021-02-06 19:20:56 +00:00
R. RyanTM 0adfe0f108 picard-tools: 2.24.1 -> 2.24.2 2021-02-05 12:35:00 +00:00
Phillip Cloud bba47f95f1 sortmerna: mark broken on darwin 2021-01-26 12:55:33 -05:00
Pavol Rusnak a6ce00c50c
treewide: remove stdenv where not needed 2021-01-25 18:31:47 +01:00
Sandro ad445d3728
Merge pull request #110735 from jbedo/bedtools 
bedtools: 2.29.2 -> 2.30.0
 2021-01-25 11:04:30 +01:00
Ryan Mulligan afebf1cc9a
Merge pull request #110529 from r-ryantm/auto-update/picard-tools 
picard-tools: 2.24.0 -> 2.24.1
 2021-01-24 18:06:28 -08:00
Justin Bedo d81e79af15
bedtools: 2.29.2 -> 2.30.0 2021-01-25 13:06:22 +11:00
volth bc0d605cf1 treewide: fix double quoted strings in meta.description 
Signed-off-by: Ben Siraphob <bensiraphob@gmail.com>
 2021-01-24 19:56:59 +07:00
Pavol Rusnak 90f7338112
treewide: stdenv.lib -> lib 2021-01-24 01:49:49 +01:00
Markus Kowalewski 6dba41fbcb
mpi: use mpi attribute consistently as the default MPI implementations 
Use the attribute mpi to provide a system wide default MPI
implementation. The default is openmpi (as before).
This now allows for overriding the MPI implentation by using
the overlay mechanism. Build all packages with mpich instead
of the default openmpi can now be achived like this:
self: super:
 {
   mpi = super.mpich;
 }

All derivations that have been using "mpi ? null" to provide optional
building with MPI have been change in the following way to allow for
optional builds with MPI:
{ ...
, mpi
, useMpi ? false
}
 2021-01-23 12:15:13 +01:00
R. RyanTM e1ea0a237a picard-tools: 2.24.0 -> 2.24.1 2021-01-22 19:10:27 +00:00
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 seems to have accidentally changed mkDerivation function for dfilemanager and solarus-quest-editor so I have reverted that here.
 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