From 20050d08b1d6b18f437d7ac44a4720f2c24d7f53 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Mon, 7 Feb 2022 14:37:43 +1100
Subject: pizzly: init
---
default.nix | 1 +
tools/pizzly-app.nix | 30 ++++++++++++++++++++++++++++++
tools/pizzly-call.nix | 24 ++++++++++++++++++++++++
tools/pizzly.nix | 8 ++++++++
4 files changed, 63 insertions(+)
create mode 100644 tools/pizzly-app.nix
create mode 100644 tools/pizzly-call.nix
create mode 100644 tools/pizzly.nix
diff --git a/default.nix b/default.nix
index ab69803..1d2bad3 100644
--- a/default.nix
+++ b/default.nix
@@ -53,6 +53,7 @@ let
genmap = callBionix ./tools/genmap.nix { };
subread = callBionix ./tools/subread.nix { };
hatchet = callBionix ./tools/hatchet.nix { };
+ pizzly = callBionix ./tools/pizzly.nix { };
slurm-run = callPackage ./lib/slurm.nix { };
slurm-exec = f: x: y:
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;
+}
--
cgit v1.2.3