Makefile

# 
# Create a directory, put this make file in it
# and for now type `make bam` or `make vcf`.
#
# You also might have to change the `ADAM` variable below

TARGETS=bam vcf
.PHONY: all $(TARGETS)

all:
	@echo "usage: make <target>" && echo "    where target may be: $(TARGETS)"

ADAM=java -jar ../adam-cli/target/adam-0.9.1-SNAPSHOT.jar

ADAM_RECORD_DIR=Example-adam-record
ADAM_RECORD_WITNESS=$(ADAM_RECORD_DIR)/_SUCCESS

ADAM_PILEUP_DIR=Example-ref-oriented-adam-pileup
ADAM_PILEUP_WITNESS=$(ADAM_PILEUP_DIR)/_SUCCESS

EXAMPLE_BAM_URL=http://gasv.googlecode.com/files/
EXAMPLE_BAM_FILENAME=Example.bam

bam: $(ADAM_RECORD_WITNESS) $(ADAM_PILEUP_WITNESS)

$(EXAMPLE_BAM_FILENAME):
	curl $(EXAMPLE_BAM_URL)$(EXAMPLE_BAM_FILENAME)

$(ADAM_RECORD_WITNESS): $(EXAMPLE_BAM_FILENAME)
	$(ADAM) transform $(EXAMPLE_BAM_FILENAME) $(ADAM_RECORD_DIR)

$(ADAM_PILEUP_WITNESS): $(ADAM_RECORD_WITNESS)
	$(ADAM) reads2ref $(ADAM_RECORD_DIR) $(ADAM_PILEUP_DIR)


PSEQ_TUT_URL=https://atgu.mgh.harvard.edu/plinkseq/dist/tutorial/
PSEQ_TUT_ARCHIVE=pseq-tut1.tar.gz
SOME_VCF_FILE=data/TSI.exon.2010_09.genotypes.vcf
ADAM_VARIANT_OF_VCF_DIR=Adam-variant-TSI-exon
ADAM_VARIANT_OF_VCF_WITNESS=Adam-variant-TSI-exon/_SUCCESS

vcf: $(ADAM_VARIANT_OF_VCF_WITNESS)

$(PSEQ_TUT_ARCHIVE):
	curl -O $(PSEQ_TUT_URL)$(PSEQ_TUT_ARCHIVE)
$(SOME_VCF_FILE): $(PSEQ_TUT_ARCHIVE)
	tar xvfz $(PSEQ_TUT_ARCHIVE) $(SOME_VCF_FILE).gz && gunzip $(SOME_VCF_FILE).gz && touch $(SOME_VCF_FILE)
$(ADAM_VARIANT_OF_VCF_WITNESS): $(SOME_VCF_FILE)
	$(ADAM) vcf2adam $(SOME_VCF_FILE) $(ADAM_VARIANT_OF_VCF_DIR)