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#
# Makefie for ParsInsert
#
# ParsInsert efficiently produces both a phylogenetic tree and taxonomic classification
# for sequences for microbial community sequence analysis.
#
# This is a C++ implementation of the Parsimonious Insertion algorithm.
#
PROGRAM = ParsInsert
OBJECTS = AttrList.o Knox_Stddef.o PNode.o SeqList.o Taxonomy.o ParsInsert.o
CXX ?= g++
INCLUDES =
LIBS = -lm -lc
.SUFFIXES: .o .cpp
.cpp.o:
$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c -o $@ $<
all: $(PROGRAM)
clean:
rm -f $(PROGRAM) $(OBJECTS) *.fasta *.log *.results *.tree
TEST_OBJECTS = PNode.o AttrList.o Knox_Stddef.o Test.o
test: $(TEST_OBJECTS)
$(CXX) $(CPPFLAGS) $(CXXFLAGS) -o Test $(TEST_OBJECTS) $(LIBS) $(LDFLAGS)
Knox_Stddef.o: Knox_Stddef.cpp Knox_Stddef.h
$(PROGRAM): $(OBJECTS)
$(CXX) $(CPPFLAGS) $(CXXFLAGS) -o $(PROGRAM) $(OBJECTS) $(LIBS) $(LDFLAGS)
TEST_DIR = ./TestData
test_short = short1000_NAST
test_set = set1000
TAXONOMY = $(TEST_DIR)/rdp.taxonomy
TREE = $(TEST_DIR)/core_rdp.ntree
TREE_SEQ = $(TEST_DIR)/core_rdp.fasta
# create compressed version of the release
RELEASE_VER = 1.04
RELEASE:
tar -czf ../ParsInsert.$(RELEASE_VER).tgz *
# use simple scoring function (-d0), threshold cutoff at 80% (-c80), only display best location (-n1)
test_options = -d0 -c80 -n1
TEST: $(PROGRAM)
rm -f $(test_set).fasta
cp TestData/$(test_set).fasta .
./$(PROGRAM) $(test_options) \
-m $(TEST_DIR)/lanemask.txt\
-x $(TAXONOMY) \
-l $(test_set).log \
-o $(test_set).results \
-t $(TREE) \
-s $(TREE_SEQ) \
$(test_set).fasta
diff $(test_set).results TestData/$(test_set).results
echo Differences:
diff $(test_set).results TestData/$(test_set).results | wc -l
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