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Makefile
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BRANCH:=`git rev-parse --abbrev-ref HEAD` ## get active GIT branch
BRANCH:=$(strip $(BRANCH))
TAG=$(BRANCH)
ARG=
run: sass version rm.locks
Rscript dev/run_app.R
run.headless:
Rscript dev/run_app_headless.R
run.tee:
Rscript dev/run_app.R 2>&1 | tee -a run.log
run.profvis:
Rscript dev/run_app_profvis.R
sass: FORCE
Rscript dev/sass.R
Rscript dev/create_source_all.R
clean: rm.locks
rm `find . -name '.#*' -o -name '*~' -o -name '#*#' -o -name '*.save' -o -name '*.bak' -o -name '*.SAVE' -o -name '*.BAK'`
rm.locks:
find . -name 'LOCK*' -exec rm {} \;
show.branch:
@echo $(BRANCH)
docker.run:
@echo running docker *$(TAG)* at port 4000
docker run --rm -it -p 4000:3838 bigomics/omicsplayground:$(TAG)
docker.run2:
@echo running docker $(TAG) at port 4000
docker run --rm -it -p 4000:3838 \
-v ~/Playground/pgx:/omicsplayground/data \
-v ~/Playground/libx-v4:/omicsplayground/libx \
-v ~/Playground/pgx-visreport:/pgx-visreport \
-v /aws/pgx-share:/omicsplayground/data_shared \
-v /aws/pgx-public:/omicsplayground/data_public \
-v ~/Playground/omicsplayground/etc:/omicsplayground/etc \
bigomics/omicsplayground:$(TAG)
docker: FORCE version
@echo building docker $(BRANCH)
docker build $(ARG) --no-cache --build-arg BRANCH=$(BRANCH) \
--progress plain \
-f docker/Dockerfile \
-t bigomics/omicsplayground:$(BRANCH) . \
2>&1 | tee docker.log
update_playdata=false
update_bigdash=false
update_playbase=true
docker.update: FORCE
@echo building update docker
docker build --no-cache \
--progress plain \
--build-arg update_playdata=$(update_playdata) \
--build-arg update_bigdash=$(update_bigdash) \
--build-arg update_playbase=$(update_playbase) \
-f docker/Dockerfile.update \
-t bigomics/omicsplayground:update .
docker.test: FORCE
@echo building test docker
docker build --no-cache \
--progress plain \
-f docker/Dockerfile.test \
-t bigomics/omicsplayground:test .
docker.bash:
@echo bash into docker $(TAG)
docker run -it bigomics/omicsplayground:$(TAG) /bin/bash
doc: FORCE
Rscript dev/02_doc.R
install: FORCE
Rscript dev/requirements.R
renv: FORCE
R -e "renv::activate();renv::restore()"
FORCE: ;
DATE = `date +%y%m%d|sed 's/\ //g'`
VERSION = "v3.5.0"
BUILD := $(VERSION)"+"$(BRANCH)""$(DATE)
version: FORCE
@echo "new version ->" $(BUILD)
echo $(BUILD) > VERSION
changelog:
sh ./dev/create-changelog.sh '.*' 3 > CHANGELOG.md
sh ./dev/create-changelog.sh '.*' 999 > CHANGELOG-full.md
sh ./dev/create-changelog.sh 'feat' 3 > FEATURES.md
sh ./dev/create-changelog-pr.sh 1 4 > CHANGELOG-pr.md
tags: version changelog
git tag -f -a $(VERSION) -m 'version $(VERSION)'
git push && git push --tags
push.latest:
docker tag bigomics/omicsplayground:$(BRANCH) bigomics/omicsplayground:latest
docker push bigomics/omicsplayground:latest
push.version:
docker tag bigomics/omicsplayground:$(BRANCH) bigomics/omicsplayground:$(VERSION)
docker push bigomics/omicsplayground:$(VERSION)
auth=none
board.launch:
R -e "options(board = '$(board)', authentication = '$(auth)'); shiny::runApp('dev/board.launch')"
board.example:
R -e "options(board = '$(board)', use_example_data = TRUE, authentication = '$(auth)'); shiny::runApp('dev/board.launch')"
pgx.check.error: sass
Rscript dev/board_check_across_pgx.R $(if $(d),-d $(d),)
app.test: sass
R -e "options(authentication='$(auth)'); shiny::runTests()"
app.test.review:
R -e "testthat::snapshot_review('snapshot/')"
update:
Rscript dev/update_packages.R