trigger #25
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| name: Liat Workflow | |
| on: | |
| push: | |
| branches: | |
| - liats/wip/ci_cd | |
| permissions: | |
| id-token: write | |
| contents: read | |
| jobs: | |
| create-conda-env: | |
| runs-on: ubuntu-latest | |
| container: | |
| image: amazonlinux:2 | |
| steps: | |
| - name: Show OS version | |
| run: cat /etc/os-release | |
| - name: Check user | |
| run: | | |
| whoami | |
| echo "HOME: $HOME" | |
| echo "GITHUB_WORKSPACE: $GITHUB_WORKSPACE" | |
| echo "PATH: $PATH" | |
| export PATH=$GITHUB_WORKSPACE:$PATH | |
| echo "PATH: $PATH" | |
| # Install tar and gzip for code checkout | |
| - name: Install tar | |
| run: yum install -y tar gzip | |
| - name: Checkout Code | |
| continue-on-error: true | |
| uses: actions/checkout@v2 # Checks out the repository under $GITHUB_WORKSPACE. | |
| - name: Show workspace | |
| run: echo $GITHUB_WORKSPACE | |
| - name: Install conda | |
| run: | | |
| curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh | |
| bash Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/miniconda | |
| echo "export PATH=$HOME/miniconda/bin:$PATH" >> $HOME/.bashrc | |
| source $HOME/.bashrc | |
| conda init bash | |
| conda config --set always_yes yes --set changeps1 no | |
| conda update -q conda | |
| conda info -a | |
| - name: Create conda environment | |
| continue-on-error: true | |
| run : | | |
| export PATH=$HOME/miniconda/bin:$PATH | |
| conda init bash | |
| conda create -n test-env python=3.10 | |
| conda activate test-env | |
| conda install pheno-utils | |
| conda list | |
| - name: Configure AWS Credentials | |
| uses: aws-actions/configure-aws-credentials@v4 | |
| with: | |
| role-to-assume: arn:aws:iam::081569964966:role/github_cicd | |
| aws-region: eu-west-1 | |
| - name: Create and Upload Artifact to S3 | |
| run: | | |
| # Example of creating a tar.gz archive and uploading it | |
| echo "Uploading artifact to S3" | |
| # tar -czvf artifact.tar.gz /path/to/your/files | |
| # aws s3 cp artifact.tar.gz s3://YOUR_S3_BUCKET_NAME/path/to/upload/ |