separate test jobs for 10x versions (83627f27) · Commits · github_fork / Universc

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

+11 −1

Original line number	Diff line number	Diff line
		@@ -50,5 +50,15 @@ jobs:
		push: false
		- name: 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
		- 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

+21 −1

Original line number	Diff line number	Diff line
		@@ -52,6 +52,27 @@ jobs:
		- name: Status
		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:
		@@ -93,4 +114,3 @@ jobs:
		push: false
		- name: Test 10x
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x_gh_actions.sh

test/run_tests_10x_gh_actions.sh

+0 −27

Original line number	Diff line number	Diff line
		@@ -17,39 +17,12 @@ bash launch_universc.sh -t "10x" --setup

		## test 10x 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

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

test/run_tests_cellranger_gh_actions.sh

0 → 100755

+52 −0

Original line number	Diff line number	Diff line
		#!/bin/bash

		# run tests in universc directory (parent of test directory)
		cd $(dirname ${BASH_SOURCE[0]})/..
		pwd

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

		rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0
		rm -rf test/cellranger_reference/cellranger-tiny-ref/3.0.0
		make test/cellranger_reference/cellranger-tiny-ref reference
		rm -rf test/cellranger_reference/cellranger-tiny-ref/1.2.0

		# reset barcodes for test
		bash launch_universc.sh -t "10x" --setup

		## test 10x 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

Admin message