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#@(#)Makefile 2021-05-22 A.J.Travis and A.Douglas
#
# pique: parallel identification of QTL's using EMMAX
#
# A software pipeline for performing GWAS (Genome Wide Association Studies)
#
# installation directory
DIR = /usr/local/pique
EMMAX = /usr/bin/emmax
PLINK = /usr/bin/p-link
EIGENSTRAT = /usr/lib/eigensoft/smartpca
R = /usr/bin/R
FORECAST = /usr/lib/R/site-library/forecast
PARALLEL = /usr/share/perl5/Parallel
READONLY = /usr/share/perl5/Readonly.pm
BIN = bin/GWAS_manhattanplots bin/pique-input bin/pique-run
ETC = etc/profile.d/EIGENSOFT.sh etc/profile.d/pique.sh
TARGETS = $(EMMAX) $(PLINK) $(EIGENSTRAT) $(R) $(FORECAST) $(READONLY) $(PARALLEL) $(BIN) $(ETC)
help:
@echo 'Type "sudo make install" to install "pique"'
all: $(TARGETS)
# install pique
install: $(TARGETS)
install -d $(DIR)/bin $(DIR)/doc
install -C -o root -g root bin/* $(DIR)/bin
install -C -o root -g root etc/profile.d/* /etc/profile.d
# perl scripts
#pique-input: bin/pique-input
#pique-run: bin/pique-run
# install "EMMAX"
$(EMMAX):
apt install emmax
emmax-beta-07Mar2010.tar.gz:
wget http://genetics.cs.ucla.edu/emmax/$@
# install PLINK
$(PLINK):
apt install plink
plink_linux_x86_64.zip:
wget https://www.cog-genomics.org/static/bin/plink161202/$@
# install "EIGENSOFT"
#$(EIGENSTRAT): EIG5.0.2.tar.gz
# tar xvf $<
# install -d /usr/local/EIGENSOFT/bin
# install -C -o root -g root EIG5.0.2/bin/* /usr/local/EIGENSOFT/bin
#
#EIG5.0.2.tar.gz:
# wget http://cdn1.sph.harvard.edu/wp-content/uploads/sites/181/2014/05/$@
$(EIGENSTRAT):
apt install eigensoft
# install R
$(R):
echo "Please install R"...
# install CRAN forecast library
$(FORECAST):
apt install r-cran-forecast
# install Parallel::ForkManager
$(PARALLEL):
apt install libparallel-forkmanager-perl
# install Perl Readonly module
$(READONLY):
apt install libreadonly-perl
%.pdf: %.odt
lowriter --headless --convert-to pdf $< --outdir $$(dirname $<)
clean:
rm -f *.log
clobber: clean
rm -rf EIG5.0.2* emmax-beta-07Mar2010*
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