Merge branch 'master' of github.com:minoda-lab/universc (b2e32a92) · Commits · github_fork / Universc

.gitattributes

+4 −0

Original line number	Diff line number	Diff line
		@@ -53,3 +53,7 @@ test/shared/indrop-v3-test/Undetermined_S0_L002_R4_001.fastq.gz filter=lfs diff=
		test/shared/indrop-v3-test/Undetermined_S0_L001_R1_001.fastq.gz filter=lfs diff=lfs merge=lfs -text
		test/shared/dropseq-test/SRR1873277_Sample1_R1.fastq.gz filter=lfs diff=lfs merge=lfs -text
		test/shared/dropseq-test/SRR1873277_Sample1_R2.fastq.gz filter=lfs diff=lfs merge=lfs -text
		test/shared/smartseq3-test/Smartseq3_diySpike_I1.fastq.gz filter=lfs diff=lfs merge=lfs -text
		test/shared/smartseq3-test/Smartseq3_diySpike_I2.fastq.gz filter=lfs diff=lfs merge=lfs -text
		test/shared/smartseq3-test/Smartseq3_diySpike_R1.fastq.gz filter=lfs diff=lfs merge=lfs -text
		test/shared/smartseq3-test/Smartseq3_diySpike_R2.fastq.gz filter=lfs diff=lfs merge=lfs -text

.github/workflows/docker-ci.yml

+5 −6

Original line number	Diff line number	Diff line
		@@ -50,7 +50,7 @@ jobs:
		push: true


		run:
		diagnostics:
		runs-on: ubuntu-20.04
		steps:
		- uses: actions/checkout@v2
		@@ -73,17 +73,16 @@ jobs:
		- name: Repo diagnostics
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls -d */
		- name: Repo size
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd; du -sckh --max=depth=1 *
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd; du -ckh -d 1 *
		- name: Parent directory diagnostics
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls -d ../*/
		- name: Parent directory size
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd; du -sckh --max-depth=1 ../*
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd; du -ckh -d 1 ../*
		- name: Grandparent directory diagnostics
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls -d ../../*/
		- name: Grandarent directory size
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd; du -sckh --max-depth=2 ../../*
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd; du -ckh -d 2 ../../*
		- name: Root directory diagnostics
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd;ls -d /*/
		- name: Root directory size
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest pwd; du -sckh --max-depth=1 /*

		run: df -h

.github/workflows/docker-run.yml

deleted100644 → 0

+0 −13

Original line number	Diff line number	Diff line
		name: Docker Compose Actions
		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"
		- name: Build diagnostics
		run: pwd; ls ../; ls ../../

.github/workflows/docker-run.yml.backup

+1 −1

Original line number	Diff line number	Diff line
		name: Docker Compose Actions Workflow
		name: Docker Compose Build
		on: push
		jobs:
		test:

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

+14 −6

Original line number	Diff line number	Diff line
		@@ -36,12 +36,14 @@ jobs:
		image: tomkellygenetics/universc:latest
		run: echo "hello from universc"
		- name: Call UniverSC from image
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x_gh_actions.sh
		timeout-minutes: 15
		run: timeout 10 docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x_gh_actions.sh \|\| code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi
		- name: Call UniverSC from container
		timeout-minutes: 15
		uses: addnab/docker-run-action@v1
		with:
		image: tomkellygenetics/universc:latest
		run: bash /universc/test/run_tests_10x_gh_actions.sh
		run: timeout 10 bash /universc/test/run_tests_10x_gh_actions.sh \|\| code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

		build:
		runs-on: ubuntu-20.04
		@@ -70,8 +72,12 @@ jobs:
		file: ./Dockerfile
		tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest
		push: false
		- name: Test 10x timeout
		timeout-minutes: 10
		run: timeout 10 docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_cellranger_gh_actions.sh \|\| code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi
		- name: Test 10x
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x_gh_actions.sh
		timeout-minutes: 10
		run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_cellranger_gh_actions.sh

		test-10x-v2:
		runs-on: ubuntu-20.04
		@@ -92,7 +98,8 @@ jobs:
		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
		timeout-minutes: 15
		run: timeout 10 docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x_v2_gh_actions.sh \|\| code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

		test-10x:
		runs-on: ubuntu-20.04
		@@ -113,4 +120,5 @@ jobs:
		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
		timeout-minutes: 15
		run: timeout 10 docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:latest bash /universc/test/run_tests_10x_gh_actions.sh \|\| code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

Admin message