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authorJustin Bedo <cu@cua0.org>2020-08-25 15:13:13 +1000
committerJustin Bedo <cu@cua0.org>2020-08-25 15:15:35 +1000
commit2cee6ee61240fbbc7f9684208b67eae8634404bf (patch)
tree0609a94a17f571f7fec905fc1cf0e1ba06a75ed0
parent1db4fdf05830358c62de3734565c33b0a377d10b (diff)
whisper: app expression merged into nixpkgs
-rw-r--r--tools/whisper-align.nix2
-rw-r--r--tools/whisper-app.nix41
-rw-r--r--tools/whisper-index.nix2
-rw-r--r--tools/whisper.nix1
4 files changed, 2 insertions, 44 deletions
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;
}