blob: 608fa9b464f3dc80e388d6051ec04d77bf5262db (
plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
|
{nixpkgs ? import <nixpkgs> {}}:
let
inherit (nixpkgs) fetchurl callPackage;
bionix = nixpkgs.lib.makeExtensible (self:
let callBionix = file: attrs: import file ({ bionix = self; } // attrs);
in with self; {
callBionix = callBionix;
id = x: x;
exec = f: x: y: f x y;
callBionixE = p: exec (callBionix p);
types = callBionix ./lib/types.nix {};
bowtie = callBionix ./tools/bowtie.nix {};
bwa = callBionix ./tools/bwa.nix {};
cnvkit = callBionix ./tools/cnvkit.nix {};
compression = callBionix ./tools/compression.nix {};
crumble = callBionix ./tools/crumble.nix {};
facets = callBionix ./tools/facets.nix {};
fastqc = callBionix ./tools/fastqc.nix {};
gridss = callBionix ./tools/gridss.nix {};
infercnv = callBionix ./tools/infercnv.nix {};
kallisto = callBionix ./tools/kallisto.nix {};
mosdepth = callBionix ./tools/mosdepth.nix {};
mutect = callBionix ./tools/mutect.nix {};
minimap2 = callBionix ./tools/minimap2.nix {};
platypus = callBionix ./tools/platypus.nix {};
ref = callBionix ./lib/references.nix {};
samtools = callBionix ./tools/samtools.nix {};
snap = callBionix ./tools/snap.nix {};
snpeff = callBionix ./tools/snpeff.nix {};
strelka = callBionix ./tools/strelka.nix {};
ascat = callBionix ./tools/ascat.nix {};
sbatch = attrs: bionix.extend (self: super: with self; rec {
sbatchDefs = { ppn = 1; mem = 1; walltime = "24:00:00"; partition = null; slurmFlags = null; } // attrs;
sbatch = attrs: (callPackage ./lib/sbatch.nix {}) (sbatchDefs // attrs);
exec = f: x: y: sbatch (builtins.intersectAttrs sbatchDefs x) (f (builtins.removeAttrs x (builtins.attrNames sbatchDefs)) y);
});
qsub = attrs: bionix.extend (self: super: with self; rec {
qsubDefs = { ppn = 1; mem = 1; walltime = "24:00:00"; tmpDir = "/tmp"; sleepTime = 60; queue = null; qsubFlags = null; } // attrs;
qsub = attrs: (callPackage ./lib/qsub.nix {}) (qsubDefs // attrs);
exec = f: x: y: qsub (builtins.intersectAttrs qsubDefs x) (f (builtins.removeAttrs x (builtins.attrNames qsubDefs)) y);
});
def = f: defs: attrs: f (defs // attrs);
pipe = let g = fs: with builtins; let h = head fs; t = tail fs; in if t != [] then x: (g t (h x)) else h; in g;
link = {src, dst}: ''
d=$(dirname ${dst})
if [ ! -e $out/$d ] ; then
mkdir -p $out/$d
fi
ln -s ${src} $out/${dst}
'';
mkLinks = nixpkgs.lib.concatMapStringsSep "\n" link;
linkDrv = x: nixpkgs.stdenvNoCC.mkDerivation {
name = "link";
buildCommand = mkLinks x;
};
ln = x: y: { src = x; dst = y; };
# Fetching files of specific type
fetchFastQ = attrs: with types; tagFiletype (filetype.fq {}) (fetchurl attrs);
fetchFastA = attrs: with types; tagFiletype (filetype.fa {}) (fetchurl attrs);
fetchFastQGZ = attrs: with types; tagFiletype (filetype.gz (filetype.fq {})) (fetchurl attrs);
fetchFastAGZ = attrs: with types; tagFiletype (filetype.gz (filetype.fa {})) (fetchurl attrs);
# Export nixpkgs and standard library lib
pkgs = nixpkgs;
lib = nixpkgs.lib // { types = types; };
stage = x@{ name, ... }: { multicore = false; } // nixpkgs.stdenvNoCC.mkDerivation (x // {name = "bionix-" + name;});
# splitting/joining
splitFile = file: drv: stage {
name = "split-${file}";
buildCommand = "ln -s ${drv}/${file} $out";
};
split = drv: lib.mapAttrs (p: _: splitFile p drv) (builtins.readDir drv);
join = drvs: stage {
name = "join";
buildCommand = ''
mkdir $out
${builtins.concatStringsSep "\n" (builtins.attrValues (lib.mapAttrs (n: d: "ln -s ${d} $out/${n}") drvs))}
'';
};
each = f: drv: join (lib.mapAttrs (_: f) (split drv));
});
in bionix
|
