Created
April 16, 2014 23:02
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# | |
# 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) |
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