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-rw-r--r--default.nix307
1 files changed, 188 insertions, 119 deletions
diff --git a/default.nix b/default.nix
index 32aa232..34059f1 100644
--- a/default.nix
+++ b/default.nix
@@ -1,134 +1,203 @@
-{nixpkgs ? import <nixpkgs> {}}:
+{ 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);
+ 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 {};
+ 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 {};
+ 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 = attrs: bionix.extend (self: super: with self; rec {
- slurmDefs = { ppn = 1; mem = 1; walltime = "24:00:00"; partition = null; slurmFlags = null; salloc = "/usr/bin/salloc"; srun = "/usr/bin/srun"; } // attrs;
- slurm = attrs: (callPackage ./lib/slurm.nix {}) (slurmDefs // attrs);
- exec = f: x: y: slurm (builtins.intersectAttrs slurmDefs x) (super.exec f (builtins.removeAttrs x (builtins.attrNames slurmDefs)) 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; 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);
+ slurm = attrs:
+ bionix.extend (self: super:
+ with self; rec {
+ slurmDefs = {
+ ppn = 1;
+ mem = 1;
+ walltime = "24:00:00";
+ partition = null;
+ slurmFlags = null;
+ salloc = "/usr/bin/salloc";
+ srun = "/usr/bin/srun";
+ } // attrs;
+ slurm = attrs:
+ (callPackage ./lib/slurm.nix { }) (slurmDefs // attrs);
+ exec = f: x: y:
+ slurm (builtins.intersectAttrs slurmDefs x) (super.exec f
+ (builtins.removeAttrs x (builtins.attrNames slurmDefs)) 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;
+ 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 \n" + (concatStringsSep "\n" (mapAttrsToList link x));
- };
+ 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));
+ };
- # 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);
+ # 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;
+ # 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 = ''
+ # 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
+ 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
- fi
- }
- for o in $outputs ; do
- rewriteOutput $o
- done
- '';
- in drv.overrideAttrs (attrs:
- if attrs ? buildCommand then
- {buildCommand = attrs.buildCommand + stripCommand;}
- else
- { fixupPhase = (if attrs ? fixupPhase then attrs.fixupPhase else "") + stripCommand; }
- );
+ '';
+ in drv.overrideAttrs (attrs:
+ if attrs ? buildCommand then {
+ buildCommand = attrs.buildCommand + stripCommand;
+ } else {
+ fixupPhase = (if attrs ? fixupPhase then attrs.fixupPhase else "")
+ + stripCommand;
+ });
+
+ # splitting/joining
+ splitFile = file: drv:
+ stage {
+ name = "split-${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));
+ });
- # 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
+ 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