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Makefile
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Makefile
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.PHONY : deps install uninstall clean pear test
deps :
@# Make dependencies directory
@mkdir deps
@# Clone and compile flahs2
@printf "\n**** Cloning flash2 from GitHub ****\n\n"
git clone https://github.com/dstreett/FLASH2.git deps/flash_dir
@printf "\n**** Compiling flash2 ****\n\n"
@cd deps/flash_dir; make; mv flash2 ..
@rm -rf deps/flash_dir
@# Clone and compile sickle
@printf "\n**** Cloning sickle from GitHub ****\n\n"
git clone https://github.com/najoshi/sickle.git deps/sickle_dir
@printf "\n**** Compiling sickle ****\n\n"
@cd deps/sickle_dir; make; mv sickle ..
@rm -rf deps/sickle_dir
pear :
@# Clone and compile pear
@printf "\n**** Cloning pear from GitHub ****\n\n"
git clone https://github.com/xflouris/PEAR.git deps/pear_dir
@printf "\n**** Compiling pear ****\n\n"
@cd deps/pear_dir; ./autogen.sh; ./configure; make; mv src/pear ..
@rm -rf deps/pear_dir
install :
@cp deps/sickle deps/flash2 fluidigm2purc crunch_clusters pacbio_err.py /usr/local/bin
@#export PATH=$PATH:$(pwd)
@#CURDIR=$(pwd)
@#printf "\nTo keep these scripts in your \044PATH, add\n\nexport PATH=\044PATH:${CURDIR}\n\nto your .bash_profile.\n\n"
uninstall :
@rm -i /usr/local/bin/sickle /usr/local/bin/flash2 /usr/local/bin/pear /usr/local/bin/fluidigm2purc /usr/local/bin/crunch_clusters
clean :
@rm -rf deps
test :
@sickle pe --help
@flash2 --help
@fluidigm2purc -h
@crunch_clusters -h
@pacbio_err.py -h
@cd tests; fluidigm2purc -f TEST