From 7372c27ea3930ad464b05a6c3ab4fd6348eb3abd Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Thu, 25 May 2023 11:50:52 +1000
Subject: ampliconarchitect: init

---
 default.nix       |  1 +
 tools/aa-app.nix  | 57 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
 tools/aa-call.nix | 31 ++++++++++++++++++++++++++++++
 tools/aa.nix      |  7 +++++++
 4 files changed, 96 insertions(+)
 create mode 100644 tools/aa-app.nix
 create mode 100644 tools/aa-call.nix
 create mode 100644 tools/aa.nix

diff --git a/default.nix b/default.nix
index 62b6d3c..529dddd 100644
--- a/default.nix
+++ b/default.nix
@@ -55,6 +55,7 @@ let
       hatchet = callBionix ./tools/hatchet.nix { };
       pizzly = callBionix ./tools/pizzly.nix { };
       quip = callBionix ./tools/quip.nix { };
+      ampliconarchitect = callBionix ./tools/aa.nix { };
 
       slurm-run = callPackage ./lib/slurm.nix { };
       slurm-exec = f: x: y:
diff --git a/tools/aa-app.nix b/tools/aa-app.nix
new file mode 100644
index 0000000..4b782b3
--- /dev/null
+++ b/tools/aa-app.nix
@@ -0,0 +1,57 @@
+{
+  stdenv,
+  fetchurl,
+  fetchFromGitHub,
+  python3,
+}: let
+  python = python3.withPackages (pkgs:
+    with pkgs; [
+      numpy
+      scipy
+      pysam
+      matplotlib
+      future
+      (mosek pkgs)
+    ]);
+
+  mosek = assert stdenv.system == "x86_64-linux";
+    pkgs:
+      pkgs.buildPythonPackage {
+        pname = "mosek";
+        version = "8.1.0.83";
+        src = fetchurl {
+          url = "https://download.mosek.com/stable/8.1.0.83/mosektoolslinux64x86.tar.bz2";
+          sha256 = "sha256-d/S/IalmQwizWYZ89ZskUoVAaXWYszuw7w+w0Vp+13k";
+        };
+        doCheck = false;
+        preBuild = ''
+          cd 8/tools/platform/linux64x86/python/3/
+        '';
+        propagatedBuildInputs = with pkgs; [numpy];
+        postInstall = ''
+          find $out -name lib\*.so\* -print0 | xargs -0 \
+            patchelf --add-rpath ${stdenv.cc.cc.lib}/lib
+        '';
+      };
+in
+  stdenv.mkDerivation rec {
+    pname = "AmpliconArchitect";
+    version = "1.3";
+
+    src = fetchFromGitHub {
+      owner = "virajbdeshpande";
+      repo = pname;
+      rev = "40da8520a953810ad43e5a6fdf4aba7449d7f5e0";
+      sha256 = "sha256-4SAOpdjXiZFTfpD6WpLfs2zDyGT2hcWabl+sUjboBpc=";
+    };
+
+    doBuild = false;
+    installPhase = ''
+      mkdir -p $out/libexec
+      cp -r src $out/libexec/aa
+      mkdir $out/bin
+      ln -s $out/libexec/aa/{AmpliconArchitect,amplified_intervals,ref_util,downsample}.py $out/bin
+    '';
+
+    buildInputs = [python];
+  }
diff --git a/tools/aa-call.nix b/tools/aa-call.nix
new file mode 100644
index 0000000..1c6a121
--- /dev/null
+++ b/tools/aa-call.nix
@@ -0,0 +1,31 @@
+{
+  bionix,
+  seeds,
+  license,
+  flags ? "",
+  downsample ? 0.1,
+  ...
+}: input:
+with bionix; let
+  indexedBam = linkOutputs {
+    "input.bam" = input;
+    "input.bam.bai" = samtools.index {} input;
+  };
+in
+  stage {
+    name = "aa-call";
+    MOSEKLM_LICENSE_FILE = license;
+    buildInputs = [bionix.ampliconarchitect.app];
+    buildCommand = ''
+      mkdir $out
+      export AA_DATA_REPO=$TMPDIR
+      tar -xzf ${self.aa.ref}
+      AmpliconArchitect.py \
+        --bam ${indexedBam}/input.bam \
+        --bed ${seeds} \
+        --ref GRCh38 \
+        --out $out/out \
+        --downsample ${toString downsample} \
+        $flags
+    '';
+  }
diff --git a/tools/aa.nix b/tools/aa.nix
new file mode 100644
index 0000000..6010c43
--- /dev/null
+++ b/tools/aa.nix
@@ -0,0 +1,7 @@
+{bionix}:
+with bionix;
+
+{
+  app = pkgs.callPackage ./aa-app.nix { };
+  call = callBionixE ./aa-call.nix { };
+}
-- 
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