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