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authorJustin Bedo <cu@cua0.org>2023-05-25 11:50:52 +1000
committerJustin Bedo <cu@cua0.org>2023-10-10 13:26:17 +1100
commit7372c27ea3930ad464b05a6c3ab4fd6348eb3abd (patch)
tree02e578175470bf5a095469bb1e2a1f1bb0f5db2c /tools
parent59edb7d9c37a688c8c408508c1a9ae5d37df348f (diff)
ampliconarchitect: init
Diffstat (limited to 'tools')
-rw-r--r--tools/aa-app.nix57
-rw-r--r--tools/aa-call.nix31
-rw-r--r--tools/aa.nix7
3 files changed, 95 insertions, 0 deletions
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 { };
+}