CalCEN/Makefile at master · maomlab/CalCEN · GitHub

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.ONESHELL:

PREFIX=~/opt

install_prerequisites:
# sratoolkit
	git clone git@github.com:ncbi/ngs.git
	pushd ngs
	./configure --prefix=${PREFIX}
	make
	make install
	popd

	pushd ngs/ngs-sdk
	./configure --prefix=${PREFIX}
	make
	make install
	popd

	git clone git@github.com:ncbi/ncbi-vdb.git
	pushd ncbi-vdb
	./configure --prefix=${PREFIX}
	make
	make install
	popd

	git clone git@github.com:ncbi/sra-tools.git
	cd sra-tools
	./configure --prefix=${PREFIX}
	make
	make install
	popd

# bowtie2
	wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.3.4.1/bowtie2-2.3.4.1-linux-x86_64.zip
	unzip bowtie2-2.3.4.1-linux-x86_64.zip
	pushd bin
	ln -s ../bowtie2-2.3.4.1-linux-x86_64/bowtie2* .
	popd

# RSEM
	git clone git@github.com:deweylab/RSEM.git
	pushd RSEM
	make
	make install DESTDIR=${PREFIX} prefix=${PREFIX}
	popd


install:
	Rscript -e "devtools::install_local('.', force = TRUE)"

test:
	Rscript -e "devtools::check()"
	Rscript -e "covr::package_coverage()"
	Rscript -e "lintr::lint_package()"
	Rscript -e "urlchecker::url_check()"
	Rscript -e "docreview::package_review()"
	Rscript -e "spelling::spell_check_package()"

test_alt_builds:
# this will email the package developer
	Rscript -e "devtools::check_win_devel(quiet = TRUE)"
	Rscript -e "devtools::check_win_release(quiet = TRUE)"
	Rscript -e "devtools::check_win_release(quiet = TRUE)"
	Rscript -e "devtools::check_mac_release(quiet = TRUE)"

# call rhub::validate_email_first(email = <email>) first
	Rscript -e "devtools::check_rhub()"
	Rscript -e "revdepcheck::revdep_check(num_workers = 4)"

CalCEN:
	cp vignettes/CalCEN/parameters_template.R parameters.R
	Rscript scripts/1_define_runs.R
	Rscript scripts/2_download_runs.R
	Rscript scripts/3_reference_genome.R
	Rscript scripts/4_submit_estimate_expression.R
	Rscript scripts/5_gather_estimated_expression.R
	Rscript scripts/6.1.1_collect_estimated_expression_meta.R
	Rscript scripts/6.1.2_build_coexp_network.R
	Rscript scripts/6.1.3_rna_seq_quality_control.R


.PHONY: install_prerequisites install test test_alt_builds CalCEN