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makefile
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ALL= phylogeo_sankoff_general \
contract_short_branch \
phylogeo_sankoff_general_dna \
mutation-samples \
alignment-filter \
partition-by-name \
sampling-by-name \
sample-and-partition-by-name \
sample-evenly \
tree-build-as-pangolin \
rename-alignment-ids \
compare-partitions \
split_tree_general
CONDA_PREFIX=/home/hforoughmand/miniconda3/envs/covid-uk/
SRC=src/
BIN=build
#ALL: $(join $(addsuffix $(BIN), $(dir $(SOURCE)))
ALL: $(BIN) $(addprefix $(BIN)/, $(ALL))
$(BIN)/phylogeo_sankoff_general: $(SRC)/phylogeo_sankoff_general.cc $(SRC)/tree.h $(SRC)/state.h
g++ $(SRC)/phylogeo_sankoff_general.cc -o $@ -O2 -std=c++11 -Wall -lboost_program_options
$(BIN)/contract_short_branch: $(SRC)/contract_short_branch.cc $(SRC)/tree.h $(SRC)/state.h
g++ $(SRC)/contract_short_branch.cc -o $@ -O2 -std=c++11 -Wall -lboost_program_options
$(BIN)/phylogeo_sankoff_general_dna: $(SRC)/phylogeo_sankoff_general_dna.cc $(SRC)/tree.h $(SRC)/state.h
g++ $(SRC)/phylogeo_sankoff_general_dna.cc -o $@ -O2 -std=c++11 -Wall -lboost_program_options
#g++ $(SRC)/phylogeo_sankoff_general_dna.cc -o $@ -O2 -std=c++11 -Wall -lboost_program_options -lboost_iostreams -I$(CONDA_PREFIX)/include -Wl,-rpath-link=$(CONDA_PREFIX)/lib -L$(CONDA_PREFIX)/lib
$(BIN)/mutation-samples: $(SRC)/mutation-samples.cc
g++ $(SRC)/mutation-samples.cc -o $@ -O2 -std=c++11 -Wall -lboost_program_options
$(BIN)/tree-stat: $(SRC)/tree-stat.cc $(SRC)/tree.h
g++ -o $@ $(SRC)/tree-stat.cc -O0 -Wall -std=c++11 -lboost_program_options
$(BIN)/alignment-filter: $(SRC)/alignment-filter.cc $(SRC)/fasta.h
g++ -o $@ $(SRC)/alignment-filter.cc -O3 -Wall -std=c++11 -lboost_iostreams -I$(CONDA_PREFIX)/include -L$(CONDA_PREFIX)/lib -Wl,-rpath-link=$(CONDA_PREFIX)/lib
$(BIN)/partition-by-name: $(SRC)/partition-by-name.cc $(SRC)/tree.h
g++ -o $@ $(SRC)/partition-by-name.cc -O0 -Wall -std=c++11 -lboost_iostreams -I$(CONDA_PREFIX)/include -lboost_program_options
$(BIN)/sampling-by-name: $(SRC)/sampling-by-name.cc $(SRC)/tree.h
g++ -o $@ $(SRC)/sampling-by-name.cc -O2 -Wall -std=c++11 -lboost_iostreams -I$(CONDA_PREFIX)/include -lboost_program_options
$(BIN)/sample-and-partition-by-name: $(SRC)/sample-and-partition-by-name.cc $(SRC)/tree.h
g++ -o $@ $(SRC)/sample-and-partition-by-name.cc -O2 -Wall -std=c++11 -lboost_iostreams -I$(CONDA_PREFIX)/include -lboost_program_options
$(BIN)/sample-evenly: $(SRC)/sample-evenly.cc $(SRC)/tree.h $(SRC)/rangetree.h
g++ -o $@ $(SRC)/sample-evenly.cc -O2 -Wall -std=c++11 -lboost_program_options -I$(CONDA_PREFIX)/include -L$(CONDA_PREFIX)/lib
$(BIN)/tree-build-as-pangolin: $(SRC)/tree-build-as-pangolin.cc $(SRC)/tree.h
g++ -o $@ $(SRC)/tree-build-as-pangolin.cc -O2 -Wall -std=c++11 -lboost_program_options
$(BIN)/rename-alignment-ids: $(SRC)/rename-alignment-ids.cc $(SRC)/tree.h
g++ -o $@ $(SRC)/rename-alignment-ids.cc -O2 -Wall -std=c++11
$(BIN)/compare-partitions: $(SRC)/compare-partitions.cc $(SRC)/tree.h
g++ -o $@ $(SRC)/compare-partitions.cc -std=c++11 -O2 -lboost_program_options
$(BIN)/split_tree_general: $(SRC)/split_tree_general.cc $(SRC)/tree.h $(SRC)/state.h
g++ -o $@ $(SRC)/split_tree_general.cc -std=c++11 -O2 -lboost_program_options
$(BIN):
mkdir build/
clean:
rm -rf $(ALL)