pizzly: init

3 files changed, 62 insertions, 0 deletions

diff --git a/tools/pizzly-app.nix b/tools/pizzly-app.nix
new file mode 100644
index 0000000..703e4aa
--- /dev/null
+++ b/tools/pizzly-app.nix
@@ -0,0 +1,30 @@
+{ lib, stdenv, fetchFromGitHub, cmake, zlib }:
+
+stdenv.mkDerivation rec {
+  pname = "pizzly";
+  version = "0.37.3";
+
+  src = fetchFromGitHub {
+    repo = pname;
+    owner = "pmelsted";
+    rev = "v${version}";
+    sha256 = "sha256-VB3kYjnhg9+QMdCAbYAzf30kO8zXZlEvK913ALZiUwU=";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ zlib ];
+
+  installPhase = ''
+    runHook preInstall
+    install -Dm 755 pizzly $out/bin/pizzly
+    runHook postInstall
+  '';
+
+  meta = with lib; {
+    description = "Fusion detection from kallisto";
+    homepage = "https://github.com/pmelsted/pizzly";
+    license = licenses.bsd2;
+    platforms = platforms.linux;
+    maintainers = with maintainers; [ jbedo ];
+  };
+}
diff --git a/tools/pizzly-call.nix b/tools/pizzly-call.nix
new file mode 100644
index 0000000..72e23bf
--- /dev/null
+++ b/tools/pizzly-call.nix
@@ -0,0 +1,24 @@
+{ bionix, kmerSize ? 31, gtf, cdna, alignScore ? 2, maxInsertSize ? 400 }:
+
+with bionix;
+with pkgs;
+
+input:
+stage {
+  name = "pizzly";
+  buildInputs = [ bionix.pizzly.app ];
+  buildCommand = ''
+    ln -s ${gtf} ref.gtf
+    ln -s ${cdna} ref.fa
+    mkdir $out
+    pizzly                          \
+      -G ref.gtf                    \
+      -C cache                      \
+      -F ref.fa                     \
+      -k ${toString kmerSize}       \
+      -o $out/output                \
+      -a ${toString alignScore}     \
+      -i ${toString maxInsertSize}  \
+      ${input}/fusion.txt
+  '';
+}
diff --git a/tools/pizzly.nix b/tools/pizzly.nix
new file mode 100644
index 0000000..4011424
--- /dev/null
+++ b/tools/pizzly.nix
@@ -0,0 +1,8 @@
+{ bionix }:
+
+with bionix;
+
+{
+  app = pkgs.callPackage ./pizzly-app.nix { };
+  call = callBionixE ./pizzly-call.nix;
+}