From 2cee6ee61240fbbc7f9684208b67eae8634404bf Mon Sep 17 00:00:00 2001
From: Justin Bedo <cu@cua0.org>
Date: Tue, 25 Aug 2020 15:13:13 +1000
Subject: whisper: app expression merged into nixpkgs

---
 tools/whisper-align.nix |  2 +-
 tools/whisper-app.nix   | 41 -----------------------------------------
 tools/whisper-index.nix |  2 +-
 tools/whisper.nix       |  1 -
 4 files changed, 2 insertions(+), 44 deletions(-)
 delete mode 100644 tools/whisper-app.nix

(limited to 'tools')

diff --git a/tools/whisper-align.nix b/tools/whisper-align.nix
index 5620fe3..c44205a 100644
--- a/tools/whisper-align.nix
+++ b/tools/whisper-align.nix
@@ -20,7 +20,7 @@ let
 
 in stage {
   name = "whisper-mem";
-  buildInputs = [ whisper.app ];
+  buildInputs = with pkgs; [ whisper ];
   buildCommand = ''
     ln -s ${fa ref} ref.fa
     for f in ${bionix.whisper.index indexAttrs ref}/* ; do
diff --git a/tools/whisper-app.nix b/tools/whisper-app.nix
deleted file mode 100644
index c3f6445..0000000
--- a/tools/whisper-app.nix
+++ /dev/null
@@ -1,41 +0,0 @@
-{ stdenv, fetchFromGitHub, fetchurl }:
-
-stdenv.mkDerivation {
-  pname = "whisper";
-  version = "2.0";
-
-  src = fetchFromGitHub {
-    owner = "refresh-bio";
-    repo = "Whisper";
-    rev = "v2.0";
-    sha256 = "100p2pqhli123wnqkxrvjcwnmlvcp1rk63whh121jannnw81rh2m";
-  };
-
-  patches = [ (fetchurl {
-    url = "https://github.com/refresh-bio/Whisper/commit/9ad77e7de68d91d9427cfbe6211e83cea89206ab.patch";
-    sha256 = "0i1s70rq5z4b3yik76vs1cxri4n3mpgfn91k35b3mwzhpxvfh7nn";}) ];
-
-  preConfigure = ''
-    cd src
-
-    # disable default static linking
-    sed -i 's/ -static / /' makefile
-  '';
-
-  installPhase = ''
-    mkdir -p $out/bin
-    cp whisper whisper-index $out/bin
-  '';
-
-  buildPhase = "make -j $NIX_BUILD_CORES";
-
-  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.linux;
-  };
-
-}
-
diff --git a/tools/whisper-index.nix b/tools/whisper-index.nix
index 675af7d..a9162f3 100644
--- a/tools/whisper-index.nix
+++ b/tools/whisper-index.nix
@@ -12,7 +12,7 @@ assert (matchFiletype "whisper-index" { fa = _: true; } ref);
 
 stage {
   name = "whisper-index";
-  buildInputs = [ whisper.app ];
+  buildInputs = with pkgs; [ whisper ];
   buildCommand = ''
     ln -s ${ref} ref.fa
     mkdir $out
diff --git a/tools/whisper.nix b/tools/whisper.nix
index 244a410..b729675 100644
--- a/tools/whisper.nix
+++ b/tools/whisper.nix
@@ -3,7 +3,6 @@
 with bionix;
 
 rec {
-  app = pkgs.callPackage ./whisper-app.nix {};
   index = callBionixE ./whisper-index.nix;
   align = callBionixE ./whisper-align.nix;
 }
-- 
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