Bump MUSCLE to 5.2 (#51881)

Co-authored-by: Martin Grigorov <martin-g@users.noreply.github.com>

recipes/muscle/build.sh

@@ -1,9 +1,18 @@
 #!/bin/bash
+set -e
 
-cd src/
-sed -i.bak -e 's/ -static//' Makefile
+mkdir -p ${PREFIX}/bin
+cd src || exit 1
+echo "0" > gitver.txt
 
-make CXX=$CXX
+cp ${RECIPE_DIR}/vcxproj_make.py .
+chmod +x vcxproj_make.py
+./vcxproj_make.py --openmp --cppcompiler ${CXX}
 
-mkdir -p "$PREFIX"/bin
-cp "$(uname)"/muscle "$PREFIX"/bin/muscle
+# Verify binary exists and is executable
+if [ ! -x ../bin/muscle ]; then
+    echo "Error: muscle binary not found"
+    exit 1
+fi
+
+cp ../bin/muscle ${PREFIX}/bin/muscle

recipes/muscle/meta.yaml

@@ -1,18 +1,18 @@
 {% set name = "muscle" %}
-{% set version = "5.1.0" %}
+{% set version = "5.2" %}
 
 package:
   name: {{ name|lower }}
   version: {{ version }}
 
 source:
-  url: https://github.com/rcedgar/muscle/archive/refs/tags/{{ version }}.tar.gz
-  sha256: 2bba8b06e3ccabf6465fa26f459763b2029d7e7b9596881063e3aaba60d9e87d
+  url: https://github.com/rcedgar/muscle/archive/refs/tags/v{{ version }}.tar.gz
+  sha256: 7aff1473241a36da94a88f37920a343fae91d2b6faae22e15c06591d1d0339b6
   patches:
     - support-linux-aarch64.patch
 
 build:
-  number: 1
+  number: 0
   run_exports:
     - {{ pin_subpackage(name, max_pin="x.x") }}
 
@@ -30,7 +30,7 @@ about:
   home: https://github.com/rcedgar/muscle
   license: GPL-3.0-only
   license_file: LICENSE
-  summary: "MUSCLE: multiple sequence alignment with high accuracy and high throughput"
+  summary: Multiple sequence and structure alignment with top benchmark scores scalable to thousands of sequences
 
 extra:
   additional-platforms:

recipes/muscle/support-linux-aarch64.patch

@@ -1,10 +1,10 @@
-diff --git i/src/myutils.h w/src/myutils.h
-index 49d28ef..8e8167e 100644
---- i/src/myutils.h
-+++ w/src/myutils.h
-@@ -11,7 +11,7 @@
- #define TRACK_ALLOC		0
- #define ALLOC_TOTALS	0
+diff --git a/src/myutils.h b/src/myutils.h
+index a5d8a58..fbf6f9f 100644
+--- a/src/myutils.h
++++ b/src/myutils.h
+@@ -10,7 +10,7 @@
+ #include <cstddef>
+ #include "myalloc.h"
 
 -#if defined(__x86_64__) || defined(_M_X64) || defined(__arm64__)
 +#if defined(__x86_64__) || defined(_M_X64) || defined(__arm64__) || defined(__aarch64__)

recipes/muscle/vcxproj_make.py

@@ -0,0 +1,225 @@
+#!/usr/bin/env python
+
+import argparse
+import os
+import sys
+
+Usage = (
+    "Convert Visual Studio .vcxproj file in current directory to Makefile and run make."
+)
+
+AP = argparse.ArgumentParser(description=Usage)
+
+# Value opts
+AP.add_argument(
+    "--std",
+    required=False,
+    help="C++ standard option for GCC, e.g. c++11 or c++17 (default none)",
+)
+AP.add_argument(
+    "--cppcompiler",
+    required=False,
+    default="g++",
+    help="C++ compiler command name default g++)",
+)
+AP.add_argument(
+    "--ccompiler",
+    required=False,
+    default="gcc",
+    help="C++ compiler command name default gcc)",
+)
+
+# Flag opts
+AP.add_argument("--debug", required=False, action="store_true", help="Debug build")
+AP.add_argument("--openmp", required=False, action="store_true", help="Requires OMP")
+AP.add_argument(
+    "--pthread", required=False, action="store_true", help="Requires pthread"
+)
+AP.add_argument("--lrt", required=False, action="store_true", help="Requires lrt")
+AP.add_argument(
+    "--symbols",
+    required=False,
+    action="store_true",
+    help="Debug symbols (default if --debug)",
+)
+AP.add_argument(
+    "--nostrip",
+    required=False,
+    action="store_true",
+    help="Don't strip symbols (default if --debug or --symbols)",
+)
+
+Args = AP.parse_args()
+debug = Args.debug
+std = Args.std
+cppcompiler = Args.cppcompiler
+ccompiler = Args.ccompiler
+nostrip = debug or Args.symbols
+symbols = debug or Args.symbols
+
+ProjFileName = None
+HdrNames = []
+for FileName in os.listdir("."):
+    if FileName.endswith(".vcxproj"):
+        ProjFileName = FileName
+    elif FileName.endswith(".h"):
+        HdrNames.append(FileName)
+if ProjFileName is None:
+    sys.stderr.write("\nProject file not found in current directory\n")
+    sys.exit(1)
+
+binary = ProjFileName.replace(".vcxproj", "")
+sys.stderr.write("binary=" + binary + "\n")
+
+compiler_opts = " -ffast-math -march=native"
+linker_opts = " -ffast-math -march=native"
+
+if std:
+    compiler_opts += " --std=" + std
+
+if debug:
+    compiler_opts += " -O0 -DDEBUG"
+    linker_opts += " -O0"
+else:
+    compiler_opts += " -O3 -DNDEBUG"
+    linker_opts += " -O3"
+
+if symbols:
+    compiler_opts += " -g3"
+    linker_opts += " -g3"
+
+if Args.openmp:
+    compiler_opts += " -fopenmp"
+    linker_opts += " -fopenmp"
+
+if Args.pthread:
+    compiler_opts += " -pthread"
+    linker_opts += " -lpthread"
+
+rc = os.system(r"rm -rf o/ ../bin/%s*" % binary)
+if rc != 0:
+    sys.stderr.write("\n\nERROR -- failed to clean\n\n")
+    sys.exit(1)
+sys.stderr.write("clean done.\n")
+
+OBJDIR = "o"
+BINDIR = "../bin"
+
+Fields = ProjFileName.split("/")
+n = len(Fields)
+Name = Fields[n - 1]
+Fields = Name.split(".")
+binary = Fields[0]
+
+CXXNames = []
+CNames = []
+with open(ProjFileName) as File:
+    for Line in File:
+        Line = Line.strip()
+        Line = Line.replace('"', "")
+        Line = Line.replace(" ", "")
+        # <ClCompile Include="betadiv.cpp" />
+        if Line.startswith("<ClCompileInclude"):
+            Fields = Line.split("=")
+            if len(Fields) != 2:
+                continue
+            FileName = Fields[1]
+            FileName = FileName.replace("/>", "")
+            if FileName.endswith(".cpp"):
+                FileName = FileName.replace(".cpp", "")
+                CXXNames.append(FileName)
+            elif FileName.endswith(".c"):
+                FileName = FileName.replace(".c", "")
+                CNames.append(FileName)
+
+assert len(CXXNames) > 0 or len(CNames) > 0
+
+with open("Makefile", "w") as f:
+
+    def Out(s):
+        print(s, file=f)
+
+    BINPATH = "$(BINDIR)/%s" % (binary)
+
+    Out("######################################################")
+    Out("# Makefile is generated by " + sys.argv[0])
+    Out("# Don't edit the Makefile -- update the python script")
+    Out("######################################################")
+    Out("")
+    Out("BINDIR := %s" % BINDIR)
+    Out("OBJDIR := %s" % OBJDIR)
+    Out("BINPATH := %s" % BINPATH)
+
+    if CNames:
+        Out("")
+        Out("CC = " + ccompiler)
+        Out("CFLAGS := $(CFLAGS) " + compiler_opts)
+
+    if CXXNames:
+        Out("")
+        Out("CXX = " + cppcompiler)
+        Out("CXXFLAGS := $(CFLAGS) " + compiler_opts)
+
+    Out("")
+    Out("UNAME_S := $(shell uname -s)")
+    Out("LDFLAGS := $(LDFLAGS) " + linker_opts)
+    Out("ifeq ($(UNAME_S),Linux)")
+    Out("    LDFLAGS += -static")
+    Out("endif")
+
+    Out("")
+    Out("HDRS = \\")
+    for Name in sorted(HdrNames):
+        Out("  %s \\" % Name)
+
+    Out("")
+    Out("OBJS = \\")
+    for Name in CXXNames:
+        Out("  $(OBJDIR)/%s.o \\" % (Name))
+
+    for Name in CNames:
+        Out("  $(OBJDIR)/%s.o \\" % (Name))
+
+    Out("")
+    Out(".PHONY: clean")
+
+    Out("")
+    Out("$(BINPATH) : $(BINDIR)/ $(OBJDIR)/ $(OBJS)")
+
+    if len(CXXNames) > 0:
+        Cmd = "\t$(CXX) $(LDFLAGS) $(OBJS) -o $(BINPATH)"
+    else:
+        Cmd = "\t%(CC) $(LDFLAGS) $(OBJS) -o $(BINPATH)"
+
+    if Args.lrt:
+        Cmd += " -lrt"
+    Out(Cmd)
+
+    if not nostrip:
+        Out("	strip $(BINPATH)")
+
+    Out("")
+    Out("$(OBJDIR)/ :")
+    Out("	mkdir -p $(OBJDIR)/")
+
+    Out("")
+    Out("$(BINDIR)/ :")
+    Out("	mkdir -p $(BINDIR)/")
+
+    if CNames:
+        Out("")
+        Out("$(OBJDIR)/%.o : %.c $(HDRS)")
+        Out("	$(CC) $(CPPFLAGS) $(CFLAGS) -c -o $@ $<")
+
+    if CXXNames:
+        Out("")
+        Out("$(OBJDIR)/%.o : %.cpp $(HDRS)")
+        Out("	$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c -o $@ $<")
+
+sys.stderr.write("Makefile done.\n")
+
+rc = os.system("make")
+if rc != 0:
+    sys.stderr.write("\n\nERROR -- make failed\n\n")
+    sys.exit(1)
+sys.stderr.write("make done.\n")