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#@(#)Makefile 2025-04-30 A.J.Travis and A.Douglas, last modified by Étienne Mollier
#
# PIQUE - Parallel Identification Of QTL's using EMMAX
#
PLINK = plink1.9
PIQUE-INPUT = pique-input
PIQUE-RUN = pique-run
PHENO_GROUP = rice_phenotype_group.txt
PHENO = rice_phenotype.txt
PLOT_FILES = plot_files.txt
IPREFIX = sativas413
OPREFIX = sativas_GWAS
TPREFIX = sativas_GWAS_trans
GPREFIX = sativas_group_GWAS
GROUPS = ADMIX AUS IND TEJ TRJ
THREADS = 16
OPT = -d -v
TEST := $(dir $(realpath $(firstword $(MAKEFILE_LIST))))
PATH := $(realpath $(TEST)/../bin):$(PATH)
help:
@echo "Targets:"
@echo "\tinput"
@echo "\trun"
@echo "\ttrans"
@echo "\tgroup"
@echo "\ttest_vcf"
@echo "\tld"
@echo "\tblocks"
@echo "\tplot"
@echo "\tall"
all: input run trans group test_vcf ld blocks plot
input: $(IPREFIX).ped
$(PIQUE-INPUT) $(OPT) -i $(IPREFIX) -o $(OPREFIX) -p $(PHENO) -k -c -e 5
touch input
run: input
$(PIQUE-RUN) $(OPT) -i $(OPREFIX) -k IBS -c $(OPREFIX).covar -n $(THREADS)
touch run
trans: $(IPREFIX).ped
rm -rf $(TPREFIX)
$(PIQUE-INPUT) $(OPT) -i $(IPREFIX) -o $(TPREFIX) -p $(PHENO) -k -c -e 5
$(PIQUE-RUN) $(OPT) -i $(TPREFIX) -k IBS -c $(TPREFIX).covar -n $(THREADS) -t BC
group: $(IPREFIX).ped
rm -rf $(GPREFIX)
$(PIQUE-INPUT) $(OPT) -i $(IPREFIX) -o $(GPREFIX) -p $(PHENO_GROUP) -k -c -e 5
$(PIQUE-RUN) $(OPT) -i $(GPREFIX) -k IBS -c $(GPREFIX).covar -n $(THREADS)
for group in $(GROUPS); do \
prefix=$(GPREFIX)\_$$group; \
$(PIQUE-RUN) $(OPT) -i $$prefix -k IBS -n $(THREADS); \
done
$(IPREFIX).ped $(IPREFIX).map:
tar xf RiceDiversity_44K_Genotypes_PLINK.tar.xz
mv -i ./RiceDiversity_44K_Genotypes_PLINK/sativas* .
rmdir RiceDiversity_44K_Genotypes_PLINK
test_vcf: test_vcf.vcf
rm -rf $@_GWAS
$(PIQUE-INPUT) $(OPT) -i $@ -f vcf -o $@_GWAS -p $(PHENO) -k -c -e 5
$(PIQUE-RUN) -i $@_GWAS -k IBS -c $@_GWAS.covar -n $(THREADS)
test_vcf.vcf: $(IPREFIX).ped $(IPREFIX).map
$(PLINK) --file $(IPREFIX) --recode vcf --out $(basename $@)
ld: input
$(PLINK) --file $(IPREFIX)_recode12 --r --out $(OPREFIX)_r
$(PLINK) --file $(IPREFIX)_recode12 --r2 --out $(OPREFIX)_r2
blocks:
$(PLINK) --file $(IPREFIX)_recode12 --blocks no-pheno-req --out $(OPREFIX)_blocks
plot: $(PLOT_FILES) run
GWAS_manhattanplots -b 0.1 -q -y 12 -i $<
clean:
rm -rf RiceDiversity_44K_Genotypes_PLINK sativas413*
rm -rf __MACOSX
rm -rf $(OPREFIX)* $(TPREFIX)* $(GPREFIX)*
rm -rf test_vcf*
rm -f input run
rm -f *.bh *.png
rm -f .pversion *.log
clobber: clean
rm -f $(IPREFIX)_recode12.*
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