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| author | thyol <thyol@pm.me> | 2022-11-22 20:00:14 +0100 |
|---|---|---|
| committer | thyol <thyol@pm.me> | 2022-11-22 20:19:17 +0100 |
| commit | d7c8595f622939bdbd70e1aaf3989cdb21f3d764 (patch) | |
| tree | 246bbf1c10209f62942626f3869c2d7d8020b69c | |
| parent | df6d9466c2290648c04464775837519528219f5e (diff) | |
| download | nixpkgs-d7c8595f622939bdbd70e1aaf3989cdb21f3d764.tar nixpkgs-d7c8595f622939bdbd70e1aaf3989cdb21f3d764.tar.gz nixpkgs-d7c8595f622939bdbd70e1aaf3989cdb21f3d764.tar.bz2 nixpkgs-d7c8595f622939bdbd70e1aaf3989cdb21f3d764.tar.lz nixpkgs-d7c8595f622939bdbd70e1aaf3989cdb21f3d764.tar.xz nixpkgs-d7c8595f622939bdbd70e1aaf3989cdb21f3d764.tar.zst nixpkgs-d7c8595f622939bdbd70e1aaf3989cdb21f3d764.zip | |
muscle: 3.8.31 -> 5.1.0
| -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, 13 insertions, 43 deletions
diff --git a/pkgs/applications/science/biology/muscle/default.nix b/pkgs/applications/science/biology/muscle/default.nix index 54ff58cce71..5d83358b001 100644 --- a/pkgs/applications/science/biology/muscle/default.nix +++ b/pkgs/applications/science/biology/muscle/default.nix @@ -1,36 +1,27 @@ -{ 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; }; } 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 deleted file mode 100644 index 7f4b2129518..00000000000 --- a/pkgs/applications/science/biology/muscle/muscle-3.8.31-no-static.patch +++ /dev/null @@ -1,21 +0,0 @@ ---- 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 - |