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{ nixpkgs ? import <nixpkgs> { }, overlays ? [ ] }:
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;
exec' = f: exec (_: f) { };
exec'' = f: exec' (_: f) { };
callBionixE = p: exec (callBionix p);
types = callBionix ./lib/types.nix { };
fetchgdrive = callBionix ./lib/google.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 { };
picard = callBionix ./tools/picard.nix { };
platypus = callBionix ./tools/platypus.nix { };
ref = callBionix ./lib/references.nix { };
samtools = callBionix ./tools/samtools.nix { };
sambamba = callBionix ./tools/sambamba.nix { };
snap = callBionix ./tools/snap.nix { };
snpeff = callBionix ./tools/snpeff.nix { };
strelka = callBionix ./tools/strelka.nix { };
ascat = callBionix ./tools/ascat.nix { };
fastp = callBionix ./tools/fastp.nix { };
octopus = callBionix ./tools/octopus.nix { };
snver = callBionix ./tools/snver.nix { };
hisat2 = callBionix ./tools/hisat2.nix { };
xenomapper = callBionix ./tools/xenomapper.nix { };
manta = callBionix ./tools/manta.nix { };
delly = callBionix ./tools/delly.nix { };
lumpy = callBionix ./tools/lumpy.nix { };
lastal = callBionix ./tools/last.nix { };
whisper = callBionix ./tools/whisper.nix { };
star = callBionix ./tools/star.nix { };
slurm-run = callPackage ./lib/slurm.nix { };
slurm-exec = f: x: y:
slurm-run x (f (builtins.removeAttrs x [
"ppn"
"mem"
"walltime"
"partition"
"slurmFlags"
"salloc"
"srun"
]) y);
slurm = bionix.extend (self: super: { exec = super.slurm-run; });
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;
qsubPath = "/usr/bin";
} // attrs;
qsub = attrs: (callPackage ./lib/qsub.nix { }) (qsubDefs // attrs);
exec = f: x: y:
qsub (builtins.intersectAttrs qsubDefs x) (super.exec f
(builtins.removeAttrs x (builtins.attrNames qsubDefs)) y);
});
def = f: defs: attrs: f (defs // attrs);
linkOutputs = x:
with lib;
nixpkgs.stdenvNoCC.mkDerivation {
name = "link-outputs";
outputs = [ "out" ] ++ attrNames x;
nativeBuildInputs = [ pkgs.perl ];
buildCommand = let
recurse = x:
if x ? type && x.type == "derivation" then
x
else if builtins.typeOf x == "set" then
linkOutputs x
else
abort "linkOutputs: unsupported type";
link = dst: src: ''
ln -s ${recurse src} $(perl -e 'print $ENV{"${dst}"}') ; ln -s ${
recurse src
} $out/${dst}
'';
in ''
mkdir $out
'' + (concatStringsSep "\n" (mapAttrsToList link x));
passthru.linkInputs = x;
};
# 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);
# Turn a multi-output derivation into a list of derivations
outputDrvs = drv: map (o: lib.getAttr o drv) drv.outputs;
# Export nixpkgs and standard library lib
pkgs = nixpkgs;
lib = nixpkgs.lib // {
types = types;
shard = callBionix ./lib/shard.nix { };
};
stage = x@{ name, stripStorePaths ? true, multicore ? false, ... }:
(if stripStorePaths then strip else x: x)
(nixpkgs.stdenvNoCC.mkDerivation (x // {
name = "bionix-" + name;
inherit multicore;
}));
strip = drv:
let
stripCommand = ''
function rewrite {
sed -i 's|[A-Za-z0-9+/]\{32\}-bionix|00000000000000000000000000000000-bionix|g' $1
}
function rewriteOutput {
if [ -f ''${!1} ] ; then
rewrite ''${!1}
else
for f in $(find ''${!1} -type f) ; do
rewrite $f
done
fi
}
for o in $outputs ; do
rewriteOutput $o
done
'';
in drv.overrideAttrs (attrs:
if attrs ? buildCommand then {
buildCommand = attrs.buildCommand + stripCommand;
} else {
fixupPhase = (if attrs ? fixupPhase then attrs.fixupPhase else "")
+ stripCommand;
});
# splitting/joining
splitFile = file: drv:
stage {
name = "split-${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));
});
overlayByType = {
lambda = bionix: overlay:
bionix.extend
(self: super: nixpkgs.lib.recursiveUpdate super (overlay self super));
path = bionix: path: overlay bionix (import path);
};
overlay = bionix: overlay:
let overlayType = builtins.typeOf overlay;
in if overlayByType ? ${overlayType} then
overlayByType.${overlayType} bionix overlay
else
builtins.throw ("cannot overlay type " + overlayType);
in with nixpkgs.lib; foldl overlay bionix overlays
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