diff options
Diffstat (limited to 'pkgs/applications/science/biology/muscle')
| -rw-r--r-- | pkgs/applications/science/biology/muscle/default.nix | 35 | ||||
| -rw-r--r-- | pkgs/applications/science/biology/muscle/muscle-3.8.31-no-static.patch | 21 |
2 files changed, 56 insertions, 0 deletions
diff --git a/pkgs/applications/science/biology/muscle/default.nix b/pkgs/applications/science/biology/muscle/default.nix new file mode 100644 index 000000000000..9cbabc7ab37e --- /dev/null +++ b/pkgs/applications/science/biology/muscle/default.nix @@ -0,0 +1,35 @@ +{ stdenv, fetchurl }: + +stdenv.mkDerivation rec { + _name = "muscle"; + name = "${_name}-${version}"; + version = "3.8.31"; + + 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 + ]; + + preBuild = '' + cd ./src/ + patchShebangs mk + ''; + + installPhase = '' + install -vD muscle $out/bin/muscle + ''; + + meta = with stdenv.lib; { + description = "A multiple sequence alignment method with reduced time and space complexity"; + license = licenses.publicDomain; + 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 = stdenv.lib.platforms.linux; + }; +} diff --git a/pkgs/applications/science/biology/muscle/muscle-3.8.31-no-static.patch b/pkgs/applications/science/biology/muscle/muscle-3.8.31-no-static.patch new file mode 100644 index 000000000000..7f4b2129518d --- /dev/null +++ b/pkgs/applications/science/biology/muscle/muscle-3.8.31-no-static.patch @@ -0,0 +1,21 @@ +--- 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 + |