update makefile

WGLab · Sep 19, 2024 · c0825c3 · c0825c3
1 parent a6dfd2a
commit c0825c3
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Showing 2 changed files with 9 additions and 1 deletion.
diff --git a/.github/workflows/build-test.yml b/.github/workflows/build-test.yml
@@ -51,6 +51,8 @@ jobs:
         python --version
         conda list | grep htslib
         conda list | grep hdf5
+        ls /usr/share/miniconda/envs/longreadsum/lib | grep hts
+        ls /usr/share/miniconda/envs/longreadsum/lib | grep hdf5
         make
 
     - name: Run tests

diff --git a/Makefile b/Makefile
@@ -2,6 +2,10 @@ INCL_DIR := $(CURDIR)/include
 SRC_DIR := $(CURDIR)/src
 LIB_DIR := $(CURDIR)/lib
 
+# Set the library paths for the compiler
+LIBRARY_PATHS := -L$(LIB_DIR) -L/usr/share/miniconda/envs/longreadsum/lib
+INCLUDE_PATHS := -I$(INCL_DIR) -I/usr/share/miniconda/envs/longreadsum/include
+
 # All targets
 all: swig_build compile
 
@@ -11,4 +15,6 @@ swig_build:
 
 # Compile the C++ shared libraries into lib/
 compile:
-	python3 setup.py build_ext --build-lib $(LIB_DIR)
+	LD_LIBRARY_PATH=$(LD_LIBRARY_PATH):/usr/share/miniconda/envs/longreadsum/lib \
+	CXXFLAGS="$(INCLUDE_PATHS)" LDFLAGS="$(LIBRARY_PATHS)" python3 setup.py build_ext --build-lib $(LIB_DIR)
+	# python3 setup.py build_ext --build-lib $(LIB_DIR)