Merge pull request #15 from manulera/master

Instructions and fixes to compile in mac

Author: lorrainea

.github/workflows/compile.yaml

@@ -0,0 +1,63 @@
+name: Build MARS
+
+on:
+  push:
+    branches:
+      - master
+  workflow_dispatch:
+
+jobs:
+  build:
+    strategy:
+      matrix:
+        include:
+          - os: ubuntu-latest
+            name: Debian-Bookworm
+            container: debian:bookworm
+          - os: ubuntu-latest
+            name: Linux
+          - os: macos-latest
+            name: macOS Intel
+          - os: macos-14
+            name: macOS ARM
+
+    runs-on: ${{ matrix.os }}
+    container: ${{ matrix.container }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Dependencies (Linux - Container)
+        if: matrix.container == 'debian:bookworm'
+        run: |
+          apt-get update
+          apt-get install -y build-essential cmake unzip
+          ./pre-install.sh
+
+      - name: Install Dependencies (Linux - Native)
+        if: matrix.os == 'ubuntu-latest' && matrix.container == ''
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y build-essential cmake
+          ./pre-install.sh
+
+      - name: Install Dependencies (macOS)
+        if: startsWith(matrix.os, 'macos')
+        run: |
+          brew install cmake libomp
+          ./pre-install.sh
+
+      - name: Build
+        run: |
+          make -f Makefile
+
+      - name: Test Binary
+        run: |
+          ./mars -h | grep "Usage: mars <options>"
+
+      - name: Upload Artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: mars-${{ matrix.name }}
+          path: mars
+          retention-days: 7

.gitignore

@@ -0,0 +1,5 @@
+*.o
+libsdsl/
+sdsl-lite/
+seqan/
+mars

INSTALL

@@ -17,3 +17,12 @@ After compilation the binary `mars' will be created in the working
 directory, e.g. you may call it from this directory via
 
  S ./mars -h
+
+Compiling in M3 Mac
+===================
+
+It can be compiled with clang.
+
+You will have to install libomp to allow the flag -fopenmp to work with.
+
+   brew install libomp

Makefile

@@ -2,9 +2,30 @@ MF=     Makefile
 
 CC=     g++
 
-CFLAGS= -g -fopenmp -D_USE_OMP -msse4.2 -O3 -fomit-frame-pointer -funroll-loops  
+CFLAGS= -g -D_USE_OMP -O3 -fomit-frame-pointer -funroll-loops -pthread
+
+# Detect OS for platform-specific settings
+UNAME_S := $(shell uname -s)
+ifeq ($(UNAME_S),Darwin)
+    # macOS
+    RPATH_FLAG := -Wl,-rpath,$(PWD)/libsdsl/lib
+    # Dynamically get Homebrew prefix (libomp path)
+    BREW_PREFIX := $(shell brew --prefix libomp)
+    # OpenMP flags for macOS
+    OPENMP_FLAGS := -Xpreprocessor -fopenmp -I$(BREW_PREFIX)/include
+    OPENMP_LIBS := -L$(BREW_PREFIX)/lib -lomp
+    CFLAGS += $(OPENMP_FLAGS)
+    LFLAGS += $(OPENMP_LIBS)
+else
+    # Linux and others
+    RPATH_FLAG := -Wl,-rpath=$(PWD)/libsdsl/lib
+    CFLAGS += -fopenmp
+    LFLAGS += -fopenmp
+endif
+
+
 
-LFLAGS= -std=c++11 -I ./ -I ./libsdsl/include/ -L ./libsdsl/lib/ -lsdsl -ldivsufsort -ldivsufsort64 -Wl,-rpath=$(PWD)/libsdsl/lib
+LFLAGS= -std=c++11 -I ./ -I ./libsdsl/include/ -L ./libsdsl/lib/ -lsdsl -ldivsufsort -ldivsufsort64 $(RPATH_FLAG) $(OPENMP_LIBS)
 
 EXE=    mars
 
@@ -22,7 +43,7 @@ HD=     EBLOSUM62.h EDNAFULL.h mars.h sacsc.h ced.h nj.h RestrictedLevenshtein.h
 OBJ=    $(SRC:.cc=.o) 
 
 .cc.o: 
-	$(CC) $(CFLAGS)-c $(LFLAGS) $< 
+	$(CC) $(CFLAGS) -c $(LFLAGS) $< 
 
 all:    $(EXE)