diff --git a/.github/workflows/test_utils.yaml b/.github/workflows/test_utils.yaml deleted file mode 100644 index be15259..0000000 --- a/.github/workflows/test_utils.yaml +++ /dev/null @@ -1,36 +0,0 @@ -name: Test Changed Projects - -on: - pull_request: - branches: - - main - -jobs: - test-changed-projects: - runs-on: ubuntu-latest - - steps: - - name: Checkout code - uses: actions/checkout@v4 - with: - fetch-depth: 0 - - - name: Get changed files in root directories - uses: tj-actions/changed-files@v47.0.5 - id: changed-files - with: - dir_names: "true" - dir_names_max_depth: 1 - files: | - */** - files_ignore: | - .github/** - base_sha: ${{ github.event.pull_request.base.ref }} - - - name: Running test on changed utility - if: steps.changed-files.outputs.all_changed_files != '' - run: | - for util in ${{ steps.changed-files.outputs.all_changed_files }}; do - echo "Running test for $util" - cd $util; make test - done diff --git a/.github/workflows/tests.yaml b/.github/workflows/tests.yaml new file mode 100644 index 0000000..3c04d7b --- /dev/null +++ b/.github/workflows/tests.yaml @@ -0,0 +1,56 @@ +name: Kit tests + +on: + pull_request: + branches: + - main + +jobs: + get-changed-kits: + runs-on: ubuntu-latest + outputs: + matrix: ${{ steps.set-matrix.outputs.matrix }} + steps: + - name: Checkout code + uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - name: Get changed files in root directories + uses: tj-actions/changed-files@v47.0.5 + id: changed-files + with: + dir_names: "true" + dir_names_max_depth: 1 + files: | + */** + files_ignore: | + .github/** + base_sha: ${{ github.event.pull_request.base.ref }} + + - name: Set matrix + id: set-matrix + run: | + kits="${{ steps.changed-files.outputs.all_changed_files }}" + # Convert space-separated string to JSON array (single line) + MATRIX=$(echo $kits | jq -cR 'split(" ") | map(select(length > 0))') + echo "matrix=$MATRIX" >> $GITHUB_OUTPUT + + test-kit: + name: Test ${{ matrix.module }} + needs: [get-changed-kits] + if: ${{ needs.get-changed-kits.outputs.matrix != '[]' }} + runs-on: ubuntu-latest + strategy: + fail-fast: false + matrix: + module: ${{ fromJson(needs.get-changed-kits.outputs.matrix) }} + steps: + - name: Checkout code + uses: actions/checkout@v4 + with: + fetch-depth: 0 + + - name: Run kit test + run: | + cd ${{ matrix.module }} && make test diff --git a/Readme.md b/Readme.md index 9602a1e..673ed94 100644 --- a/Readme.md +++ b/Readme.md @@ -6,3 +6,4 @@ Genomics Kit integrates the utilities for bioinformatics analysis 2. [spark-on-slurm](./spark-on-slurm/): Spark on SLURM cluster configuration, supported 3. [GLnexus](https://github.com/dnanexus-rnd/GLnexus): The joint variant calling for cohort vcf for deepvariant gvcf 4. [DPGT](https://github.com/BGI-flexlab/DPGT): DPGT is a distributed population genetics analysis tool which enabled joint calling on millions of WGS(whole genome sequencing) samples. +5. [Hail](https://hail.is/): Powering genomic analysis, at every scale diff --git a/common.mk b/common.mk index 117d50a..6a7a4c4 100644 --- a/common.mk +++ b/common.mk @@ -1,3 +1,4 @@ .PHONY: test +HOMEDIR:=$(dir $(abspath $(lastword $(MAKEFILE_LIST)))) ${HOME}/.pixi/bin/pixi: curl -sSL https://pixi.sh/install.sh | sh \ No newline at end of file diff --git a/hail/.gitattributes b/hail/.gitattributes new file mode 100644 index 0000000..997504b --- /dev/null +++ b/hail/.gitattributes @@ -0,0 +1,2 @@ +# SCM syntax highlighting & preventing 3-way merges +pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff diff --git a/hail/.gitignore b/hail/.gitignore new file mode 100644 index 0000000..ae849e6 --- /dev/null +++ b/hail/.gitignore @@ -0,0 +1,3 @@ +# pixi environments +.pixi/* +!.pixi/config.toml diff --git a/hail/Makefile b/hail/Makefile new file mode 100644 index 0000000..ae5d3a0 --- /dev/null +++ b/hail/Makefile @@ -0,0 +1,47 @@ +include ../common.mk +SLURM_IMAGE:= nttg8100/river-slurm:1.1.0 +.PHONY: setup example clean install + +setup: ${HOME}/.pixi/bin/pixi + ${HOME}/.pixi/bin/pixi install + +start-slurm: + docker run \ + -v ${HOMEDIR}:/tmp/gkit \ + -v ${HOME}/.pixi:/root/.pixi \ + --name slurm-dev \ + -p 8081:22 \ + --rm \ + --privileged \ + -d ${SLURM_IMAGE} || echo "Docker Slurm is already configured" + +get-slurm: + @count=0; \ + max=5; \ + until [ $$count -ge $$max ]; do \ + echo "Checking SLURM (attempt $$((count+1))/$$max)..." ; \ + docker exec -w /home/river slurm-dev squeue && break; \ + count=$$((count+1)); \ + echo "SLURM not ready, retrying in 5 seconds..." ; \ + sleep 5; \ + done; \ + if [ $$count -eq $$max ]; then \ + echo "SLURM still not available after $$max attempts"; \ + exit 1; \ + fi + +install: + ${HOME}/.pixi/bin/pixi run install-sparkhpc + +# inside user river is the standard user with 1001 mapping id, Github Actions does not have this user +test: ${HOME}/.pixi/bin/pixi start-slurm get-slurm + docker exec \ + -w /tmp/gkit/hail \ + slurm-dev /root/.pixi/bin/pixi run sparkhpc-hail + +test-slurm-local: + ${HOME}/.pixi/bin/pixi run sparkhpc-example + +clean: + rm -f sparkhpc/sparkcluster-*.log sparkhpc/job + rm -f ${HOME}/.sparkhpc* diff --git a/spark-on-slurm/examples/simulate_gwas_by_hail.py b/hail/examples/simulate_gwas_by_hail.py similarity index 100% rename from spark-on-slurm/examples/simulate_gwas_by_hail.py rename to hail/examples/simulate_gwas_by_hail.py diff --git a/hail/pixi.lock b/hail/pixi.lock new file mode 100644 index 0000000..923cbd6 --- /dev/null +++ b/hail/pixi.lock @@ -0,0 +1,1959 @@ +version: 6 +environments: + default: + channels: + - 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slurm-dev /root/.pixi/bin/pixi run sparkhpc-hail + slurm-dev /root/.pixi/bin/pixi run sparkhpc-pi test-slurm-local: ${HOME}/.pixi/bin/pixi run sparkhpc-example diff --git a/spark-on-slurm/pixi.toml b/spark-on-slurm/pixi.toml index be438ea..feb1411 100644 --- a/spark-on-slurm/pixi.toml +++ b/spark-on-slurm/pixi.toml @@ -8,7 +8,6 @@ version = "0.1.0" [tasks] sparkhpc-validate = "python examples/validate_spark.py" sparkhpc-pi = "sparkcluster start 2 && python examples/pi_counter.py" -sparkhpc-hail = "sparkcluster start 2 && sleep 10 && python examples/simulate_gwas_by_hail.py" [dependencies] python = "3.11.*"