Makefile

# Required env variables:
# - LBL_PASSWORD
# - LBL_USER

.PHONY: prepare
prepare: mirror_ANIs mirror_unicycler mirror_seqs mirror_genomes

.PHONY: align
align: build/alignments.csv

build data data/ANI data/reference_genomes:
	mkdir -p $@

# 1. Download ANIm percentage identity from LBL (/data/iarpa/qc/pyani/[SAMPLE]/pyani_out/ANIm_percentage_identity.tab)
.PHONY: mirror_ANIs
	sshpass -p ${LBL_PASSWORD} rsync -avR ${LBL_USER}@merlot.lbl.gov:/data/iarpa/qc/pyani/*/pyani_out/ANIm_percentage_identity.tab .

# 2. Download unicycler_assembly genomes from LBL (/data/iarpa/TE/[SAMPLE]/assembly/unicycler_assembly.fasta)
.PHONY: mirror_unicycler
mirror_unicycler:
	sshpass -p ${LBL_PASSWORD} rsync -avRL ${LBL_USER}@merlot.lbl.gov:/data/iarpa/TE/*/assembly/unicycler_assembly.fasta .

# 3. Select best match to unicycler_assembly
build/reference_genomes.csv: src/pick_genomes.py | build
	python3 $< data/ANI $@

# 4. Download best match reference genomes from LBL (/data/iarpa/TE/[SAMPLE]/reference_genome/[GENOME_ID])
# WARNING: this will take quite some time!
.PHONY: mirror_genomes
mirror_genomes: build/reference_genomes.csv | data/reference_genomes
	$(eval CP=$(shell tail -n +2 build/reference_genomes.csv | sed -E 's|^([0-9]+),(.+)$$|/data/iarpa/TE/\1/reference_genome/\2.f*|g' | tr '\r\n' ' '))
	sshpass -p ${LBL_PASSWORD} scp -T ${LBL_USER}@merlot.lbl.gov:"$(CP)" data/reference_genomes

# 5. Download the target sequences to blast against the genomes
.PHONY: mirror_seqs
mirror_seqs:
	sshpass -p ${LBL_PASSWORD} rsync -avR ${LBL_USER}@merlot.lbl.gov:/data/iarpa/TE/*/target_sequence/IF*.fasta .

# 6. BLAST! This will also take some time - add '-v' to the command to see progress
build/alignments.csv: src/blast_seqs.py build/reference_genomes.csv
	python3 $^ $@