dhatribadri is testing snakemake workflow 🚀 #87
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| name: Test QCD Pipeline | |
| run-name: ${{ github.actor }} is testing snakemake workflow 🚀 | |
| on: | |
| push: | |
| branches: | |
| - main | |
| pull_request: | |
| branches: | |
| - main | |
| jobs: | |
| Test-QCD-Pipeline: | |
| #runs-on: ubuntu-latest | |
| runs-on: self-hosted | |
| steps: | |
| # - run: echo "🎉 The job was automatically triggered by a ${{ github.event_name }} event." | |
| # - run: echo "🐧 This job is now running on a ${{ runner.os }} server hosted by GitHub!" | |
| # - run: echo "🔎 The name of your branch is ${{ github.ref }} and your repository is ${{ github.repository }}." | |
| - name: Checkout repository | |
| uses: actions/checkout@v3 | |
| - run: echo "💡 The ${{ github.repository }} repository has been cloned to the runner." | |
| - run: echo "🖥️ The workflow is now ready to test your code on the runner." | |
| - name: List files in the repository | |
| run: | | |
| ls | |
| - name: Get working directory | |
| run: | | |
| pwd | |
| - name: Set up Miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| env: | |
| CONDA: "/Users/Dhatrib/miniconda3" | |
| with: | |
| # export CONDA="/Users/Dhatrib/miniconda3" | |
| # export PATH="$CONDA/bin:$PATH" | |
| #CONDA: "/Users/Dhatrib/miniconda3" | |
| #miniconda-version: "latest" | |
| python-version: '3.10' | |
| auto-update-conda: true | |
| activate-environment: 'qcd_env_test' | |
| environment-file: 'qcd_environment_shr.yaml' | |
| #use-channel-priority: true | |
| # - name: SSh into Actions | |
| # uses: actions/checkout@v4 | |
| # - name: Setup tmate session | |
| # uses: mxschmitt/action-tmate@v3 | |
| - name: Install pip dependencies | |
| run: | | |
| source /Users/Dhatrib/miniconda3/etc/profile.d/conda.sh | |
| conda init | |
| conda activate qcd_env_test | |
| pip install --requirement .test/requirements.txt | |
| pip install dropbox | |
| pip install --upgrade tabulate | |
| pip install --upgrade snakemake | |
| #source $CONDA/bin/activate | |
| #source ~/.bash_profile | |
| # - name: Install singularity | |
| # run: | | |
| # sudo apt-get install -y \ | |
| # autoconf \ | |
| # automake \ | |
| # cryptsetup \ | |
| # fuse \ | |
| # fuse2fs \ | |
| # git \ | |
| # libfuse-dev \ | |
| # libglib2.0-dev \ | |
| # libseccomp-dev \ | |
| # libtool \ | |
| # pkg-config \ | |
| # runc \ | |
| # squashfs-tools \ | |
| # squashfs-tools-ng \ | |
| # uidmap \ | |
| # wget \ | |
| # zlib1g-dev | |
| # - name: SSh into Actions | |
| # uses: actions/checkout@v4 | |
| # - name: Setup tmate session | |
| # uses: mxschmitt/action-tmate@v3 | |
| # ./mconfig --without-suid && \ | |
| # make -C ./builddir && \ | |
| # make -C ./builddir install | |
| - name: Install Go | |
| run: | | |
| brew install go | |
| go version | |
| - name: Install dependencies using Homebrew | |
| run: | | |
| brew install wget | |
| brew install go | |
| brew install squashfs | |
| - name: Download Singularity | |
| run: | | |
| wget https://github.com/sylabs/singularity/archive/refs/tags/v3.8.3.tar.gz | |
| tar -xzf singularity-3.8.3.tar.gz | |
| - name: Install Singularity | |
| run: | | |
| cd singularity | |
| ./mconfig | |
| make -C builddir | |
| sudo make -C builddir install | |
| - name: Verify Singularity installation | |
| run: singularity --version | |
| #https://github.com/sylabs/singularity/archive/refs/tags/v3.8.3.tar.gz | |
| # - name: Install singularity | |
| # uses: eWaterCycle/setup-singularity@v7 | |
| # with: | |
| # singularity-version: 3.8.3 | |
| # - name: Export Singularity Path | |
| # run: | | |
| # export PATH=/home/runner/go/src/github.com/hpcng/singularity-3.8.3/prefix/bin:$PATH | |
| # echo "Singularity binary: $(which singularity)" | |
| # singularity --version | |
| # # Diagnostic steps for Singularity capabilities | |
| # - name: Install dependencies for Singularity | |
| # run: | | |
| # sudo apt-get update | |
| # sudo apt-get install squashfuse fuse2fs gocryptfs | |
| # - name: Set up sysctl for unprivileged user namespaces | |
| # run: | | |
| # sudo sh -c 'echo kernel.unprivileged_userns_clone=1 > /etc/sysctl.d/90-unprivileged_userns.conf' | |
| # sudo sysctl -p /etc/sysctl.d/90-unprivileged_userns.conf | |
| # sudo sysctl --system | |
| # uname -r | |
| # sudo sh -c 'cat /proc/sys/kernel/unprivileged_userns_clone' | |
| # sudo sh -c 'ls /etc/sysctl.d/90-unprivileged_userns.conf' | |
| # - name: Verify Singularity capabilities | |
| # run: | | |
| # singularity build --sandbox ubuntu_sandbox docker://ubuntu:20.04 | |
| # singularity exec --userns ubuntu_sandbox uname -a | |
| # singularity exec --userns ubuntu_sandbox cat /proc/sys/kernel/unprivileged_userns_clone | |
| # # Debugging step: Print environment variables | |
| # - name: Print environment variables | |
| # run: printenv | |
| # Download FASTQ files from Dropbox | |
| - name: Download FASTQ files from Dropbox and copy it to local path | |
| env: | |
| DROPBOX_ACCESS_TOKEN: ${{ secrets.DROPBOX_ACCESS_TOKEN }} | |
| run: | | |
| source /Users/Dhatrib/miniconda3/etc/profile.d/conda.sh | |
| conda activate qcd_env_test | |
| export DROPBOX_ACCESS_TOKEN=${DROPBOX_ACCESS_TOKEN} | |
| python3 download_fastqs.py | |
| - name: Create necessary directories | |
| run: | | |
| mkdir -p results/2024-12-04_Project_Test_QCD_Pipeline/quality_raw | |
| mkdir -p results/2024-12-04_Project_Test_QCD_Pipeline/trimmomatic | |
| mkdir -p results/2024-12-04_Project_Test_QCD_Pipeline/raw_coverage | |
| mkdir -p results/2024-12-04_Project_Test_QCD_Pipeline/spades | |
| # - name: SSh into Actions | |
| # uses: actions/checkout@v4 | |
| # - name: Setup tmate session | |
| # uses: mxschmitt/action-tmate@v3 | |
| - name: Snakemake workflow | |
| run: | | |
| source $CONDA/bin/activate | |
| conda activate qcd_env_test | |
| snakemake -s QCD.smk -p --use-conda --use-singularity --conda-frontend conda --configfile .test/config/config.yaml --latency-wait 1000 --cores 2 | |
| # uses: snakemake/[email protected] | |
| # with: | |
| # directory: '.' | |
| # snakefile: 'QCD.smk' | |
| # # stagein: ./mconfig --without-suid && \ | |
| # # make -C ./builddir && \ | |
| # # make -C ./builddir install | |
| # args: '--cores 4 --use-conda --use-docker --use-envmodules --conda-cleanup-pkgs cache -j 999 --conda-frontend conda --configfile .test/config/config.yaml --latency-wait 1000 --singularity-args "--fakeroot"' | |
| #run: echo "🍏 This job's status is ${{ job.status }}." |