From 313959727797a511ce906411b077c989e8b9bb42 Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Wed, 22 Apr 2020 16:56:11 +1000
Subject: [PATCH] whisper: init at 2.0.1

---
 .../science/biology/whisper/default.nix       | 34 +++++++++++++++++++
 pkgs/top-level/all-packages.nix               |  2 ++
 2 files changed, 36 insertions(+)
 create mode 100644 pkgs/applications/science/biology/whisper/default.nix

diff --git a/pkgs/applications/science/biology/whisper/default.nix b/pkgs/applications/science/biology/whisper/default.nix
new file mode 100644
index 000000000000..9e336600202b
--- /dev/null
+++ b/pkgs/applications/science/biology/whisper/default.nix
@@ -0,0 +1,34 @@
+{ stdenv, fetchFromGitHub, fetchurl }:
+
+stdenv.mkDerivation rec {
+  pname = "whisper";
+  version = "2.0.1";
+
+  src = fetchFromGitHub {
+    owner = "refresh-bio";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "0wpx1w1mar2d6zq2v14vy6nn896ds1n3zshxhhrrj5d528504iyw";
+  };
+
+  preConfigure = ''
+    cd src
+
+    # disable default static linking
+    sed -i 's/ -static / /' makefile
+  '';
+
+  installPhase = ''
+    runHook preInstall
+    install -Dt $out/bin whisper whisper-index
+    runHook postInstall
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Short read sequence mapper";
+    license = licenses.gpl3;
+    homepage = "https://github.com/refresh-bio/whisper";
+    maintainers = with maintainers; [ jbedo ];
+    platforms = platforms.x86_64;
+  };
+}
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index a11116c96b22..2d636b02dddd 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -24906,6 +24906,8 @@ in
 
   varscan = callPackage ../applications/science/biology/varscan { };
 
+  whisper = callPackage ../applications/science/biology/whisper { };
+
   hmmer = callPackage ../applications/science/biology/hmmer { };
 
   bwa = callPackage ../applications/science/biology/bwa { };