Merge branch 'master' of github.com:minoda-lab/universc (28840b30) · Commits · github_fork / Universc

.github/workflows/docker-ci-runner.yml

+11 −1

Original line number	Original line	Diff line number	Diff line
	@@ -50,5 +50,15 @@ jobs:
	push: false		push: false
	- name: Hello world		- name: Hello world
	run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest echo "hello world"		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest echo "hello world"
	- name: Diagnostics		- name: Repo diagnostics
	run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls
			- name: Repo size
			run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd; du -sckh *
			- name: Parent directory diagnostics
			run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls ..
			- name: Parent directory size
			run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd; du -sckh ../*
			- name: Root directory diagnostics
			run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls /*
			- name: Root directory size
			run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd; du -sckh /*

.github/workflows/docker-test-10x.yml

+42 −0

Original line number	Original line	Diff line number	Diff line
	@@ -52,6 +52,48 @@ jobs:
	- name: Status		- name: Status
	run: echo "build complete"		run: echo "build complete"

			test-cellranger:
			runs-on: ubuntu-20.04
			steps:
			- uses: actions/checkout@v2
			- uses: docker/setup-buildx-action@v1
			- uses: docker/login-action@v1
			with:
			username: ${{ secrets.DOCKER_HUB_USERNAME }}
			password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
			registry: ${{ env.REGISTRY }}

			- name: Build and push
			uses: docker/build-push-action@v2
			with:
			context: ./
			file: ./Dockerfile
			tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest
			push: false
			- name: Test 10x
			run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x_gh_actions.sh

			test-10x-v2:
			runs-on: ubuntu-20.04
			steps:
			- uses: actions/checkout@v2
			- uses: docker/setup-buildx-action@v1
			- uses: docker/login-action@v1
			with:
			username: ${{ secrets.DOCKER_HUB_USERNAME }}
			password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
			registry: ${{ env.REGISTRY }}

			- name: Build and push
			uses: docker/build-push-action@v2
			with:
			context: ./
			file: ./Dockerfile
			tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest
			push: false
			- name: Test 10x
			run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x_v2_gh_actions.sh

	test-10x:		test-10x:
	runs-on: ubuntu-20.04		runs-on: ubuntu-20.04
	steps:		steps:

.github/workflows/docker-test-indropsv3.yml

0 → 100644

+32 −0

Original line number	Original line	Diff line number	Diff line
			name: Test inDrops v3
			on: push
			jobs:
			test:
			runs-on: ubuntu-20.04
			steps:
			- uses: actions/checkout@v2
			- name: Build the stack
			run: docker-compose up -d
			- name: Status
			run: echo "build complete"

			test-indrops-v3:
			runs-on: ubuntu-20.04
			steps:
			- uses: actions/checkout@v2
			- uses: docker/setup-buildx-action@v1
			- uses: docker/login-action@v1
			with:
			username: ${{ secrets.DOCKER_HUB_USERNAME }}
			password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
			registry: ${{ env.REGISTRY }}

			- name: Build and push
			uses: docker/build-push-action@v2
			with:
			context: ./
			file: ./Dockerfile
			tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest
			push: false
			- name: Test DropSeq
			run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_indropsv3_gh_actions.sh

.github/workflows/docker-test-smartseq3.yml

0 → 100644

+32 −0

Original line number	Original line	Diff line number	Diff line
			name: Test Smart-Seq3
			on: push
			jobs:
			test:
			runs-on: ubuntu-20.04
			steps:
			- uses: actions/checkout@v2
			- name: Build the stack
			run: docker-compose up -d
			- name: Status
			run: echo "build complete"

			test-smart-seq3:
			runs-on: ubuntu-20.04
			steps:
			- uses: actions/checkout@v2
			- uses: docker/setup-buildx-action@v1
			- uses: docker/login-action@v1
			with:
			username: ${{ secrets.DOCKER_HUB_USERNAME }}
			password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
			registry: ${{ env.REGISTRY }}

			- name: Build and push
			uses: docker/build-push-action@v2
			with:
			context: ./
			file: ./Dockerfile
			tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest
			push: false
			- name: Test DropSeq
			run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_smartseq3_gh_actions.sh

test/run_tests_10x_gh_actions.sh

+3 −66

Original line number	Original line	Diff line number	Diff line
	@@ -4,35 +4,12 @@
	cd $(dirname ${BASH_SOURCE[0]})/..		cd $(dirname ${BASH_SOURCE[0]})/..
	pwd		pwd

	# used to export to PATH for testing on SGE server
	export PATH=${HOME}/local/bin/cellranger-2.1.0:$PATH

	cellrangerversion=`cellranger count --version \| head -n 2 \| tail -n 1 \| cut -f2 -d'(' \| cut -f1 -d')'`
	cellrangerpath=`which cellranger`

	# set up cellranger reference
	if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then
	ln -h $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA
	fi
	if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then
	ln -h $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA
	fi

	# used to export to PATH for testing on SGE server
	export PATH=${HOME}/local/bin/cellranger-3.0.2:$PATH

	cellrangerversion=`cellranger count --version \| head -n 2 \| tail -n 1 \| cut -f2 -d'(' \| cut -f1 -d')'`		cellrangerversion=`cellranger count --version \| head -n 2 \| tail -n 1 \| cut -f2 -d'(' \| cut -f1 -d')'`
	cellrangerpath=`which cellranger`		cellrangerpath=`which cellranger`

	# set up cellranger reference		rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0
	if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA ]]; then		rm -rf test/cellranger_reference/cellranger-tiny-ref/3.0.0
	ln $(dirname $cellrangerpath)/cellranger-tiny-ref/3.0.0/star/SA test/cellranger_reference/cellranger-tiny-ref/3.0.0/star/SA		make test/cellranger_reference/cellranger-tiny-ref reference
	fi
	if [[ ! -f test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA ]] && [[ -f $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA ]]; then
	ln $(dirname $cellrangerpath)/cellranger-tiny-ref/1.2.0/star/SA test/cellranger_reference/cellranger-tiny-ref/1.2.0/star/SA
	fi

	rm -rf test/shared/dropseq-test/* test/shared/icell8-test/* test/shared/mappa-test/
	rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0		rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0

	# reset barcodes for test		# reset barcodes for test
	@@ -40,52 +17,12 @@ bash launch_universc.sh -t "10x" --setup

	## test 10x data		## test 10x data
	# unzip input data		# unzip input data
	ls ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt*
	if [[ ! -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt.gz ]]; then
	gzip -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt
	fi
	rm -rf ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt
	if [[ -d tiny-test ]]; then
	rm -rf tiny-test
	fi
	# test cellranger call
	if [[ $cellrangerversion == "3.0.2" ]]; then
	cellranger testrun --id="tiny-test"
	fi
	# unzip input data
	if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/*fastq.gz ]]; then
	gunzip -f test/shared/cellranger-tiny-fastq/3.0.0/*fastq.gz
	fi
	if [[ -f test/shared/cellranger-tiny-fastq/3.0.0/*fastq ]]; then
	rm -rf test/shared/cellranger-tiny-fastq/3.0.0/*fastq.gz
	fi
	# test cellranger call
	if [[ -d tiny-count-v3 ]]; then
	rm -rf tiny-count-v3
	fi
	if [[ ! -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt.gz ]]; then
	gzip -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt
	fi
	if [[ -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt ]]; then
	rm -rf ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt
	fi
	cellranger count --id="tiny-count-v3" \
	--fastqs="test/shared/cellranger-tiny-fastq/3.0.0/" --sample="tinygex" \
	--transcriptome="test/cellranger_reference/cellranger-tiny-ref/3.0.0" \
	--jobmode "local" --localcores 1
	if [[ -d tiny-count-v2 ]]; then
	rm -rf tiny-count-v2
	fi
	if [[ ! -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt.gz ]]; then		if [[ ! -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt.gz ]]; then
	gzip -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt		gzip -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt
	fi		fi
	if [[ -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt ]]; then		if [[ -f ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt ]]; then
	rm -rf ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt		rm -rf ${cellrangerpath}-cs/${cellrangerversion}/lib/python/cellranger/barcodes/3M-february-2018.txt
	fi		fi
	cellranger count --id="tiny-count-v2" \
	--fastqs="test/shared/cellranger-tiny-fastq/1.2.0/" --sample="" --chemistry="threeprime" \
	--transcriptome="test/cellranger_reference/cellranger-tiny-ref/1.2.0" \
	--jobmode "local" --localcores 1

	# call convert on 10x with multiple lanes		# call convert on 10x with multiple lanes
	if [[ -d test-10x-v3 ]]; then		if [[ -d test-10x-v3 ]]; then

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