NCBI SRA (Short Read Archive) 形式から fastq 形式に変換する Makefile ref: http://qiita.com/yk-tanigawa/items/f78834d697daf23378b0

file0.txt

## commands
FASTQ-DUMP = /somewhere/fastq-dump

## files
FASTQ1 = $(SRA:%.sra=%_1.fastq)
FASTQ2 = $(SRA:%.sra=%_2.fastq)

all: $(FASTQ1) $(FASTQ2)

# obtain the paired-end fastq files from a given sra file
$(FASTQ1) $(FASTQ2): $(SRA)
    $(FASTQ-DUMP) --qual-filter --split-files $<

file1.txt

## commands
FASTQ-DUMP = /somewhere/fastq-dump

## files
FASTQ = $(SRA:%.sra=%.fastq)

all: $(FASTQ)

# obtain the fastq file from a given sra file
$(FASTQ): $(SRA)
    $(FASTQ-DUMP) --qual-filter $<