Merge pull request #668 from KimBioInfoStudio/fix/makefile-conda-compat

build: unify static/dynamic linking for conda/package manager compatibility

Author: sfchen

.github/workflows/ci.yml

@@ -24,42 +24,45 @@ jobs:
         if: runner.os == 'Linux'
         run: |
           sudo apt-get update
-          sudo apt-get install -y build-essential libdeflate-dev nasm
+          sudo apt-get install -y build-essential nasm
 
       - name: build ISA-L static (Ubuntu)
         if: runner.os == 'Linux'
         run: |
-          git clone --depth=1 --branch v2.31.0 https://github.com/intel/isa-l.git /tmp/isa-l
+          git clone --depth=1 --branch v2.31.1 https://github.com/intel/isa-l.git /tmp/isa-l
           cd /tmp/isa-l
           ./autogen.sh
-          ./configure --prefix=/tmp/isal-install --enable-static --disable-shared
+          ./configure --prefix=/usr/local --enable-static --disable-shared
           make -j$(nproc)
-          make install
+          sudo make install
+
+      - name: build libdeflate static (Ubuntu)
+        if: runner.os == 'Linux'
+        run: |
+          git clone --depth=1 --branch v1.23 https://github.com/ebiggers/libdeflate.git /tmp/libdeflate
+          cd /tmp/libdeflate
+          cmake -B _build -DCMAKE_BUILD_TYPE=Release \
+            -DLIBDEFLATE_BUILD_STATIC_LIB=ON -DLIBDEFLATE_BUILD_SHARED_LIB=OFF \
+            -DLIBDEFLATE_BUILD_GZIP=OFF -DCMAKE_INSTALL_PREFIX=/usr/local
+          cmake --build _build -j$(nproc)
+          sudo cmake --install _build
 
       - name: install dependencies (macOS)
         if: runner.os == 'macOS'
         run: brew install libdeflate isa-l
 
-      - name: build Highway static
+      - name: build Highway
         run: |
           git clone --depth=1 --branch 1.3.0 https://github.com/google/highway.git /tmp/highway
           cd /tmp/highway
           cmake -B _build -DCMAKE_BUILD_TYPE=Release -DBUILD_SHARED_LIBS=OFF \
             -DHWY_ENABLE_TESTS=OFF -DHWY_ENABLE_EXAMPLES=OFF \
-            -DCMAKE_INSTALL_PREFIX=/tmp/hwy-install
+            -DCMAKE_INSTALL_PREFIX=/usr/local
           cmake --build _build -j$(nproc 2>/dev/null || sysctl -n hw.ncpu)
-          cmake --install _build
+          sudo cmake --install _build
 
       - name: build fastp
-        run: |
-          EXTRA_INC="" EXTRA_LIB=""
-          for prefix in /tmp/hwy-install /tmp/isal-install; do
-            [ -d "$prefix/include" ] && EXTRA_INC="$EXTRA_INC $prefix/include"
-            [ -d "$prefix/lib" ] && EXTRA_LIB="$EXTRA_LIB $prefix/lib"
-            [ -d "$prefix/lib64" ] && EXTRA_LIB="$EXTRA_LIB $prefix/lib64"
-          done
-          make -j$(nproc 2>/dev/null || sysctl -n hw.ncpu) \
-            INCLUDE_DIRS="$EXTRA_INC" LIBRARY_DIRS="$EXTRA_LIB"
+        run: make -j$(nproc 2>/dev/null || sysctl -n hw.ncpu)
 
       - name: smoke test
         run: |

Makefile

@@ -7,6 +7,15 @@ BINDIR ?= $(PREFIX)/bin
 INCLUDE_DIRS ?=
 LIBRARY_DIRS ?=
 
+# Auto-detect library paths via pkg-config (works with conda, brew, system packages)
+PKG_CONFIG ?= pkg-config
+HWY_CFLAGS := $(shell $(PKG_CONFIG) --cflags libhwy 2>/dev/null)
+HWY_LIBS := $(shell $(PKG_CONFIG) --libs-only-L libhwy 2>/dev/null)
+ISAL_CFLAGS := $(shell $(PKG_CONFIG) --cflags libisal 2>/dev/null)
+ISAL_LIBS := $(shell $(PKG_CONFIG) --libs-only-L libisal 2>/dev/null)
+DEFLATE_CFLAGS := $(shell $(PKG_CONFIG) --cflags libdeflate 2>/dev/null)
+DEFLATE_LIBS := $(shell $(PKG_CONFIG) --libs-only-L libdeflate 2>/dev/null)
+
 SRC := $(wildcard ${DIR_SRC}/*.cpp)
 OBJ := $(patsubst %.cpp,${DIR_OBJ}/%.o,$(notdir ${SRC}))
 
@@ -15,23 +24,31 @@ TARGET := fastp
 BIN_TARGET := ${TARGET}
 
 CXX ?= g++
-CXXFLAGS := -std=c++11 -pthread -g -O3 -MD -MP -I. -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) ${CXXFLAGS}
+CXXFLAGS := -std=c++11 -pthread -g -O3 -MD -MP -I. -I${DIR_INC} $(foreach includedir,$(INCLUDE_DIRS),-I$(includedir)) $(HWY_CFLAGS) $(ISAL_CFLAGS) $(DEFLATE_CFLAGS) ${CXXFLAGS}
 LIBS := -lisal -ldeflate -lhwy -lpthread
 
+PKG_LDFLAGS := $(HWY_LIBS) $(ISAL_LIBS) $(DEFLATE_LIBS)
+
 UNAME_S := $(shell uname -s)
+FIND_STATIC = $(firstword $(foreach d,$(LIBRARY_DIRS),$(wildcard $(d)/lib$(1).a)) $(wildcard /usr/local/lib/lib$(1).a /opt/homebrew/lib/lib$(1).a))
+STATIC_LIBS :=
+DYNAMIC_LIBS :=
+$(foreach lib,isal deflate hwy,\
+  $(if $(call FIND_STATIC,$(lib)),\
+    $(eval STATIC_LIBS += $(call FIND_STATIC,$(lib))),\
+    $(eval DYNAMIC_LIBS += -l$(lib))))
+
 ifeq ($(UNAME_S),Linux)
-  # Linux: fully static binary
-  LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) -static -Wl,--no-as-needed -pthread $(LIBS) $(LD_FLAGS)
+  ifeq ($(DYNAMIC_LIBS),)
+    # All .a found: fully static binary (default for Linux)
+    LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(PKG_LDFLAGS) -static -Wl,--no-as-needed -pthread $(LIBS) $(LD_FLAGS)
+  else
+    # Some .a missing (e.g. conda): link .a directly + dynamic fallback
+    LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(PKG_LDFLAGS) $(STATIC_LIBS) $(DYNAMIC_LIBS) -lpthread $(LD_FLAGS)
+  endif
 else
-  # macOS: link 3rd-party libs statically via .a when available, fallback to dynamic
-  FIND_STATIC = $(firstword $(foreach d,$(LIBRARY_DIRS),$(wildcard $(d)/lib$(1).a)) $(wildcard /usr/local/lib/lib$(1).a /opt/homebrew/lib/lib$(1).a))
-  STATIC_LIBS :=
-  DYNAMIC_LIBS :=
-  $(foreach lib,isal deflate hwy,\
-    $(if $(call FIND_STATIC,$(lib)),\
-      $(eval STATIC_LIBS += $(call FIND_STATIC,$(lib))),\
-      $(eval DYNAMIC_LIBS += -l$(lib))))
-  LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(STATIC_LIBS) $(DYNAMIC_LIBS) -lpthread $(LD_FLAGS)
+  # macOS: .a preferred, fallback to dynamic
+  LD_FLAGS := $(foreach librarydir,$(LIBRARY_DIRS),-L$(librarydir)) $(PKG_LDFLAGS) $(STATIC_LIBS) $(DYNAMIC_LIBS) -lpthread $(LD_FLAGS)
 endif
 
 

src/fastqreader.h

@@ -31,11 +31,7 @@ SOFTWARE.
 #include "common.h"
 #include <iostream>
 #include <fstream>
-#if __has_include(<isa-l/igzip_lib.h>)
 #include <isa-l/igzip_lib.h>
-#else
-#include "igzip_lib.h"
-#endif
 #include "readpool.h"
 
 class FastqReader{