muscle: 3.8.31 -> 5.1.0

{ 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";

  };

  patches = [

    ./muscle-3.8.31-no-static.patch

  ];

  src = fetchFromGitHub {

    owner = "rcedgar";

    repo = "${name}";

    rev = "${version}";

    hash = "sha256-NpnJziZXga/T5OavUt3nQ5np8kJ9CFcSmwyg4m6IJsk=";

  };

  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;

  };

}

--- 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