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{nixpkgs ? import <nixpkgs> {}}:
let
inherit (nixpkgs) fetchurl callPackage;
bionix = nixpkgs.lib.makeExtensible (self:
let callBionix = file: attrs: import file ({ bionix = self; nixpkgs = nixpkgs; } // 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 {};
bwa = callBionix ./tools/bwa.nix {};
bowtie = callBionix ./tools/bowtie.nix {};
compression = callBionix ./tools/compression.nix {};
crumble = callBionix ./tools/crumble.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 {};
platypus = callBionix ./tools/platypus.nix {};
samtools = callBionix ./tools/samtools.nix {};
strelka = callBionix ./tools/strelka.nix {};
ref = callBionix ./lib/references.nix {};
qsub = attrs: bionix.extend (self: super: with self; rec {
qsubDefs = { ppn = 1; mem = 1; walltime = "24:00:00"; tmpDir = "/tmp"; sleepTime = 60; } // 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;
# 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);
});
in bionix
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