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Makefile
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Makefile
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TAXONOMY_DIR := raw_data/
PROTEIN = output_data/protein_taxonomy.db
DEAD = output_data/dead_taxonomy.db
NUC = output_data/taxonomy.db
usage:
@echo -e "Usage:\n'make nucleotide' will create a nucleotide taxonomy db"
@echo -e "'make dead' will create a dead nucleotide taxonomy db"
@echo -e "'make protein' will create a protein taxonomy db."
@echo -e "'make vacuum' will clean up all three DBs."
@echo -e "'make clean' will remove all three DBs. \n"
all: clean nucleotide dead protein
vacuum:
./vaccum.sh $(NUC)
./vaccum.sh $(DEAD)
./vaccum.sh $(PROTEIN)
# $(DB): clean taxids nodes names hosts
nucleotide:
echo $(TAXONOMY_DIR) $(NUC)
rm -f $(NUC)
./shell/nucleotide-db.sh $(TAXONOMY_DIR)accession2taxid/ $(NUC)
./shell/add-nodes.sh $(TAXONOMY_DIR)new_taxdump/nodes.dmp $(NUC)
./shell/add-names.sh $(TAXONOMY_DIR)new_taxdump/names.dmp $(NUC)
./shell/add-hosts.sh $(TAXONOMY_DIR)new_taxdump/host.dmp $(NUC)
dead:
echo $(TAXONOMY_DIR) $(DEAD)
rm -f $(DEAD)
./shell/dead-db.sh $(TAXONOMY_DIR)accession2taxid/ $(DEAD)
./shell/add-nodes.sh $(TAXONOMY_DIR)new_taxdump/nodes.dmp $(DEAD)
./shell/add-names.sh $(TAXONOMY_DIR)new_taxdump/names.dmp $(DEAD)
./shell/add-hosts.sh $(TAXONOMY_DIR)new_taxdump/host.dmp $(DEAD)
protein:
echo $(TAXONOMY_DIR) $(PROTEIN)
rm -f $(PROTEIN)
./shell/protein-db.sh $(TAXONOMY_DIR)accession2taxid/ $(PROTEIN)
./shell/add-nodes.sh $(TAXONOMY_DIR)new_taxdump/nodes.dmp $(PROTEIN)
./shell/add-names.sh $(TAXONOMY_DIR)new_taxdump/names.dmp $(PROTEIN)
./shell/add-hosts.sh $(TAXONOMY_DIR)new_taxdump/host.dmp $(PROTEIN)
clean:
rm -f $(NUC)
rm -f $(DEAD)
rm -f $(PROTEIN)