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--- kraken2-2.14/src/Makefile 2025-02-18 09:29:30.000000000 +0530
+++ kraken2-2.14.new/src/Makefile 2025-02-19 22:39:05.587331135 +0530
@@ -1,6 +1,6 @@
CXX ?= g++
KRAKEN2_SKIP_FOPENMP ?= -fopenmp
-CXXFLAGS = $(KRAKEN2_SKIP_FOPENMP) -Wall -std=c++11 -O3
+CXXFLAGS = $(KRAKEN2_SKIP_FOPENMP) -Wall -std=c++11 -O2
CXXFLAGS += -DLINEAR_PROBING
.PHONY: all clean install
@@ -10,7 +10,7 @@
all: $(PROGS)
install: $(PROGS)
- cp $(PROGS) "$(KRAKEN2_DIR)/"
+ cp $(PROGS) $(DESTDIR)"$(KRAKEN2_DIR)/"
clean:
rm -f *.o $(PROGS)
@@ -34,19 +34,19 @@
k2mask.o: k2mask.cc gzstream.h threadpool.h
build_db: build_db.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o utilities.o
- $(CXX) $(CXXFLAGS) -o $@ build_db.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o utilities.o
+ $(CXX) $(CXXFLAGS) -o $@ $(LDFLAGS) build_db.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o utilities.o
classify: classify.o reports.o hyperloglogplus.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o aa_translate.o utilities.o
- $(CXX) $(CXXFLAGS) -o $@ classify.o reports.o hyperloglogplus.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o aa_translate.o utilities.o
+ $(CXX) $(CXXFLAGS) -o $@ $(LDFLAGS) classify.o reports.o hyperloglogplus.o mmap_file.o compact_hash.o taxonomy.o seqreader.o mmscanner.o omp_hack.o aa_translate.o utilities.o
estimate_capacity: estimate_capacity.o seqreader.o mmscanner.o omp_hack.o utilities.o
- $(CXX) $(CXXFLAGS) -o $@ estimate_capacity.o seqreader.o mmscanner.o omp_hack.o utilities.o
+ $(CXX) $(CXXFLAGS) -o $@ $(LDFLAGS) estimate_capacity.o seqreader.o mmscanner.o omp_hack.o utilities.o
dump_table: dump_table.o mmap_file.o compact_hash.o omp_hack.o taxonomy.o reports.o hyperloglogplus.o
- $(CXX) $(CXXFLAGS) -o $@ dump_table.o mmap_file.o compact_hash.o omp_hack.o taxonomy.o reports.o hyperloglogplus.o
+ $(CXX) $(CXXFLAGS) -o $@ $(LDFLAGS) dump_table.o mmap_file.o compact_hash.o omp_hack.o taxonomy.o reports.o hyperloglogplus.o
lookup_accession_numbers: lookup_accession_numbers.o mmap_file.o omp_hack.o utilities.o
- $(CXX) $(CXXFLAGS) -o $@ lookup_accession_numbers.o mmap_file.o omp_hack.o utilities.o
+ $(CXX) $(CXXFLAGS) -o $@ $(LDFLAGS) lookup_accession_numbers.o mmap_file.o omp_hack.o utilities.o
k2mask: k2mask.o seqreader.o
- $(CXX) $(CXXFLAGS) -o $@ k2mask.o seqreader.o -lz -pthread
+ $(CXX) $(CXXFLAGS) -o $@ $(LDFLAGS) k2mask.o seqreader.o -lz -pthread
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