Merge pull request #202395 from thyol/muscle

muscle: 3.8.31 -> 5.1.0

pkgs/applications/science/biology/muscle/default.nix

···
-{ lib, stdenv, fetchurl }:
+{ lib, stdenv, fetchFromGitHub }:
 
 stdenv.mkDerivation rec {
-  _name   = "muscle";
-  name    = "${_name}-${version}";
-  version = "3.8.31";
+  name   = "muscle";
+  version = "5.1.0";
 
-  src = fetchurl {
-    url = "https://www.drive5.com/muscle/downloads${version}/${_name}${version}_src.tar.gz";
-    sha256 = "1b89z0x7h098g99g00nqadgjnb2r5wpi9s11b7ddffqkh9m9dia3";
+
+  src = fetchFromGitHub {
+    owner = "rcedgar";
+    repo = "${name}";
+    rev = "${version}";
+    hash = "sha256-NpnJziZXga/T5OavUt3nQ5np8kJ9CFcSmwyg4m6IJsk=";
   };
 
-  patches = [
-    ./muscle-3.8.31-no-static.patch
-  ];
-
-  preBuild = ''
-    cd ./src/
-    patchShebangs mk
-  '';
+  sourceRoot = "source/src";
 
   installPhase = ''
-    install -vD muscle $out/bin/muscle
+    install -m755 -D Linux/muscle $out/bin/muscle
   '';
 
   meta = with lib; {
-    broken = (stdenv.isLinux && stdenv.isAarch64);
-    description = "A multiple sequence alignment method with reduced time and space complexity";
-    license     = licenses.publicDomain;
+    description = "Multiple sequence alignment with top benchmark scores scalable to thousands of sequences";
+    license     = licenses.gpl3Plus;
     homepage    = "https://www.drive5.com/muscle/";
-    maintainers = [ maintainers.unode ];
-    # NOTE: Supposed to be compatible with darwin/intel & PPC but currently fails.
-    # Anyone with access to these platforms is welcome to give it a try
-    platforms   = lib.platforms.linux;
+    maintainers = with maintainers; [ unode thyol ];
   };
 }

pkgs/applications/science/biology/muscle/muscle-3.8.31-no-static.patch

···
---- a/src/mk	2010-05-02 01:15:42.000000000 +0200
-+++ b/src/mk	2018-01-27 17:07:23.539092748 +0100
-@@ -5,14 +5,14 @@
- rm -f *.o muscle.make.stdout.txt muscle.make.stderr.txt
- for CPPName in $CPPNames
- do
--  echo $CPPName >> /dev/tty
-+  echo $CPPName
-   g++ $ENV_GCC_OPTS -c -O3 -msse2 -mfpmath=sse -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 $CPPName.cpp -o $CPPName.o  >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt
- done
- 
- LINK_OPTS=
--if [ `uname -s` == Linux ] ; then
--    LINK_OPTS=-static
--fi
-+#if [ `uname -s` == Linux ] ; then
-+#    LINK_OPTS=-static
-+#fi
- g++ $LINK_OPTS $ENV_LINK_OPTS -g -o muscle $ObjNames  >> muscle.make.stdout.txt 2>> muscle.make.stderr.txt
- tail muscle.make.stderr.txt
-