diff options
-rw-r--r-- | default.nix | 307 |
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 |