-
Notifications
You must be signed in to change notification settings - Fork 0
/
Copy pathMakefile
61 lines (47 loc) · 2.31 KB
/
Makefile
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
BASE_DIR := $(shell pwd)
REF_DIR := $(BASE_DIR)/data/ref
VEP_CACHE_DIR := $(REF_DIR)/vep_cache
BAM_DIR := $(BASE_DIR)/data/bam
BED_FILE = $(BASE_DIR)/data/targets-CYP2D6.bed
SAMPLE1 = $(BAM_DIR)/NA02016.bam
SAMPLE2 = $(BAM_DIR)/NA07439.bam
SAMPLE_SHEET = $(BASE_DIR)/data/sample_sheet.tsv
VEP_URL = https://ftp.ensembl.org/pub/release-113/variation/indexed_vep_cache/homo_sapiens_merged_vep_113_GRCh38.tar.gz
VEP_FILE = $(VEP_CACHE_DIR)/homo_sapiens_merged_vep_113_GRCh38.tar.gz
CLIN_VCF_URL = https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz
CLIN_VCF_IDX_URL = https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz.tbi
VCF_FILE = $(VEP_CACHE_DIR)/clinvar.vcf.gz
VCF_IDX_FILE = $(VEP_CACHE_DIR)/clinvar.vcf.gz.tbi
FASTA_URL = https://ftp.ensembl.org/pub/release-113/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.chromosome.22.fa.gz
FASTA_FILE = $(REF_DIR)/Homo_sapiens.GRCh38.dna.chromosome.22.fa.gz
FASTA_UNZIPPED = $(REF_DIR)/Homo_sapiens.GRCh38.dna.chromosome.22.fa
SAMPLE1_BAM = https://downloads.pacbcloud.com/public/dataset/HiFi_amplicon_CYP2D6/downsampled/NA02016.bam
SAMPLE2_BAM = https://downloads.pacbcloud.com/public/dataset/HiFi_amplicon_CYP2D6/downsampled/NA07439.bam
all: $(BED_FILE) $(FASTA_UNZIPPED) $(VEP_CACHE_DIR)/.done $(SAMPLE1) $(SAMPLE2) $(SAMPLE_SHEET)
$(SAMPLE1):
mkdir -p $(BAM_DIR)
[ -f $(SAMPLE1) ] || curl -o $(SAMPLE1) $(SAMPLE1_BAM)
$(SAMPLE2):
mkdir -p $(BAM_DIR)
[ -f $(SAMPLE2) ] || curl -o $(SAMPLE2) $(SAMPLE2_BAM)
$(BED_FILE):
mkdir -p $(REF_DIR)
printf "22\t42126499\t42130865\tCYP2D6:ENSG00000100197\t.\t-\n" > $@
$(VEP_CACHE_DIR)/.done:
[ -d $(VEP_CACHE_DIR) ] || mkdir -p $(VEP_CACHE_DIR)
[ -f $(VEP_FILE) ] || curl -o $(VEP_FILE) $(VEP_URL)
[ -f $(VCF_FILE) ] || curl -o $(VCF_FILE) $(CLIN_VCF_URL)
[ -f $(VCF_IDX_FILE) ] || curl -o $(VCF_IDX_FILE) $(CLIN_VCF_IDX_URL)
[ -f $(VEP_CACHE_DIR)/.done ] || (tar xzf $(VEP_FILE) -C $(VEP_CACHE_DIR) && rm $(VEP_FILE) && touch $(VEP_CACHE_DIR)/.done)
$(FASTA_UNZIPPED):
[ -f $(FASTA_FILE) ] || curl -o $(FASTA_FILE) $(FASTA_URL)
[ -f $(FASTA_UNZIPPED) ] || gzip -d $(FASTA_FILE)
$(SAMPLE_SHEET):
printf "name\tpath\n" > $@
printf "NA02016\t%s\n" "$(SAMPLE1)" >> $@
printf "NA07439\t%s\n" "$(SAMPLE2)" >> $@
clean:
rm -f $(BED_FILE) $(VEP_FILE) $(FASTA_FILE)
rm -rf $(VEP_CACHE_DIR)
rm -f $(FASTA_UNZIPPED)
.PHONY: clean