hatchet: include gurobi dependency if needed

1 files changed, 132 insertions, 125 deletions

diff --git a/tools/hatchet-call.nix b/tools/hatchet-call.nix
index c99e664..55414fe 100644
--- a/tools/hatchet-call.nix
+++ b/tools/hatchet-call.nix
@@ -1,131 +1,138 @@
-{ bionix
-, gurobiLicense ? null
-, count_reads ? true
-, genotype_snps ? true
-, count_alleles ? true
-, combine_counts ? true
-, cluster_bins ? true
-, plot_bins ? true
-, compute_cn ? true
-, plot_cn ? true
-, size ? "50kb"
-, mincov ? 8
-, maxcov ? 300
-, snps
-, phase ? "None"
-, diploidbaf ? 0.08
-, tolerancerdr ? 0.15
-, tolerancebaf ? 0.04
-, sizethreshold ? 0.01
-, figsize ? "6,3"
-, clones ? [ 2 6 ]
-, seeds ? 400
-, minprop ? 0.03
-, diploidcmax ? 6
-, tetraploidcmax ? 12
-, ghostprop ? 0.35
-, limitinc ? 0.6
-, blocklength ? "50kb"
+{
+  bionix,
+  gurobiLicense ? null,
+  count_reads ? true,
+  genotype_snps ? true,
+  count_alleles ? true,
+  combine_counts ? true,
+  cluster_bins ? true,
+  plot_bins ? true,
+  compute_cn ? true,
+  plot_cn ? true,
+  size ? "50kb",
+  mincov ? 8,
+  maxcov ? 300,
+  snps,
+  phase ? "None",
+  diploidbaf ? 0.08,
+  tolerancerdr ? 0.15,
+  tolerancebaf ? 0.04,
+  sizethreshold ? 0.01,
+  figsize ? "6,3",
+  clones ? [2 6],
+  seeds ? 400,
+  minprop ? 0.03,
+  diploidcmax ? 6,
+  tetraploidcmax ? 12,
+  ghostprop ? 0.35,
+  limitinc ? 0.6,
+  blocklength ? "50kb",
 }:
-
 with bionix;
 with lib;
 with types;
-
-{ normal, tumours }:
-
-let getRef = matchFiletype "hatchet" { bam = { ref, ... }: ref; };
-in
-
-assert all (x: getRef normal == getRef x) tumours;
-
-let
-  ref = getRef normal;
-
-  ini = pkgs.writeText "hatchet.ini" (generators.toINI { } {
-    run = {
-      inherit count_reads genotype_snps count_alleles combine_counts cluster_bins plot_bins compute_cn plot_cn;
-      reference = "${lnRef ref}/ref.fa";
-      normal = "${lnBam normal}/input.bam";
-      bams = concatMapStringsSep " " (x: "${lnBam x}/input.bam") tumours;
-      samples = "@SAMPLES@";
-      output = "./out";
-      processes = "@PROCESSES@";
-    };
-
-    count_reads = { inherit size; };
-    genotype_snps = {
-      inherit mincov maxcov;
-      snps = "${lnVcfBz snps}/vcf.bgz";
-    };
-
-    count_alleles = { inherit mincov maxcov; };
-    combine_counts = { inherit blocklength phase; };
-    cluster_bins = { inherit diploidbaf tolerancerdr tolerancebaf; };
-    plot_bins = { inherit sizethreshold figsize; };
-    compute_cn = {
-      inherit seeds minprop diploidcmax tetraploidcmax ghostprop limitinc;
-      clones = concatMapStringsSep "," builtins.toString clones;
-    };
-
-  });
-
-  lnRef = ref: linkOutputs {
-    "ref.fa" = ref;
-    "ref.fa.fai" = samtools.faidx { } ref;
-    "ref.dict" = samtools.dict { } ref;
-  };
-
-  lnBam = bam:
-    linkOutputs {
-      "input.bam" = bam;
-      "input.bam.bai" = samtools.index { } bam;
-    };
-
-  lnVcfBz = vcf:
-    let bz = compression.bgzip { } vcf;
+  {
+    normal,
+    tumours,
+  }: let
+    getRef = matchFiletype "hatchet" {bam = {ref, ...}: ref;};
+  in
+    assert all (x: getRef normal == getRef x) tumours; let
+      ref = getRef normal;
+
+      ini = pkgs.writeText "hatchet.ini" (generators.toINI {} {
+        run = {
+          inherit count_reads genotype_snps count_alleles combine_counts cluster_bins plot_bins compute_cn plot_cn;
+          reference = "${lnRef ref}/ref.fa";
+          normal = "${lnBam normal}/input.bam";
+          bams = concatMapStringsSep " " (x: "${lnBam x}/input.bam") tumours;
+          samples = "@SAMPLES@";
+          output = "./out";
+          processes = "@PROCESSES@";
+        };
+
+        count_reads = {inherit size;};
+        genotype_snps = {
+          inherit mincov maxcov;
+          snps = "${lnVcfBz snps}/vcf.bgz";
+        };
+
+        count_alleles = {inherit mincov maxcov;};
+        combine_counts = {inherit blocklength phase;};
+        cluster_bins = {inherit diploidbaf tolerancerdr tolerancebaf;};
+        plot_bins = {inherit sizethreshold figsize;};
+        compute_cn = {
+          inherit seeds minprop diploidcmax tetraploidcmax ghostprop limitinc;
+          clones = concatMapStringsSep "," builtins.toString clones;
+        };
+      });
+
+      lnRef = ref:
+        linkOutputs {
+          "ref.fa" = ref;
+          "ref.fa.fai" = samtools.faidx {} ref;
+          "ref.dict" = samtools.dict {} ref;
+        };
+
+      lnBam = bam:
+        linkOutputs {
+          "input.bam" = bam;
+          "input.bam.bai" = samtools.index {} bam;
+        };
+
+      lnVcfBz = vcf: let
+        bz = compression.bgzip {} vcf;
+      in
+        linkOutputs {
+          "vcf.bgz" = bz;
+          "vcf.bgz.tbi" = samtools.tabix {} bz;
+        };
+
+      getSN = let
+        script = pkgs.writeText "getSN.awk" ''
+          BEGIN{
+            FS=":"
+            RS="[ \t\n]"
+          }
+          $1=="SM"{print $2; exit}
+        '';
+      in
+        pkgs.writeShellScriptBin "getSN" ''
+          exec samtools view -H "$1" | awk -f ${script}
+        '';
     in
-    linkOutputs {
-      "vcf.bgz" = bz;
-      "vcf.bgz.tbi" = samtools.tabix { } bz;
-    };
-
-  getSN =
-    let
-      script = pkgs.writeText "getSN.awk" ''
-        BEGIN{
-          FS=":"
-          RS="[ \t\n]"
+      stage
+      ({
+          name = "HATCHet";
+          buildInputs =
+            [hatchet.app getSN pkgs.samtools pkgs.bcftools]
+            ++ (
+              if gurobiLicense == null
+              then [pkgs.cbc]
+              else [pkgs.gurobi]
+            );
+          buildCommand = ''
+            # Get tumour names
+            names="${concatMapStringsSep " " (x: "$(getSN ${x})") tumours}"
+
+            # macro substitute ini file
+            substitute ${ini} hatchet.ini \
+              --replace "@PROCESSES@" "$NIX_BUILD_CORES" \
+              --replace "@SAMPLES@" "$names"
+
+            hatchet run hatchet.ini
+
+            cp -r out $out
+          '';
+          passthru.multicore = true;
         }
-        $1=="SM"{print $2; exit}
-      '';
-    in
-    pkgs.writeShellScriptBin "getSN" ''
-      exec samtools view -H "$1" | awk -f ${script}
-    '';
-
-in
-stage
-  ({
-    name = "HATCHet";
-    buildInputs = [ hatchet.app getSN pkgs.samtools pkgs.bcftools ] ++ optional (gurobiLicense == null) pkgs.cbc;
-    buildCommand = ''
-      # Get tumour names
-      names="${concatMapStringsSep " " (x: "$(getSN ${x})") tumours}"
-
-      # macro substitute ini file
-      substitute ${ini} hatchet.ini \
-        --replace "@PROCESSES@" "$NIX_BUILD_CORES" \
-        --replace "@SAMPLES@" "$names"
-
-      hatchet run hatchet.ini
-
-      cp -r out $out
-    '';
-    passthru.multicore = true;
-  } // (if gurobiLicense != null then {
-    GRB_LICENSE_FILE = gurobiLicense;
-    HATCHET_COMPUTE_CN_SOLVER = "gurobi";
-  } else {
-    HATCHET_COMPUTE_CN_SOLVER = "cbc";
-  }))
+        // (
+          if gurobiLicense != null
+          then {
+            GRB_LICENSE_FILE = gurobiLicense;
+            HATCHET_COMPUTE_CN_SOLVER = "gurobi";
+          }
+          else {
+            HATCHET_COMPUTE_CN_SOLVER = "cbc";
+          }
+        ))