add GH workflow #2
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| --- | |
| name: test latest image | |
| on: | |
| push: | |
| branches: ['*'] | |
| schedule: | |
| - cron: 0 0 1 * * | |
| workflow_dispatch: | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| jobs: | |
| test_latest_image: | |
| strategy: | |
| matrix: | |
| dataset: ['1', '2'] | |
| fail-fast: false | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Install dependencies | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y tree | |
| - name: Clone repo | |
| uses: actions/checkout@v3 | |
| - name: pull docker image | |
| run: docker pull bids/freesurfer:latest | |
| - name: add license | |
| run: | | |
| mkdir -p ~/license | |
| echo "cHJpbnRmICJEeWxhbi5OaWVsc29uQGdtYWlsLmNvbVxuMzcwNjNcbiAqQ1lrZWhQYUNvRDlNXG4gRlM2N1BTWmRFV2lqb1xuIiA+IH4vbGljZW5zZS9saWNlbnNlLnR4dA==" | base64 -d | sh | |
| - name: print version | |
| run: | | |
| docker run -ti --rm --read-only \ | |
| bids/freesurfer:latest --version | |
| docker run -ti --rm --read-only \ | |
| bids/freesurfer:latest --help | |
| - name: get data | |
| run: | | |
| wget https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/utils/get_data_from_osf.sh | |
| bash get_data_from_osf.sh ds114_test${{ matrix.dataset }} | |
| bash get_data_from_osf.sh ds114_test${{ matrix.dataset }}_freesurfer_precomp_v6.0.0 | |
| - name: prepare output dir | |
| run: mkdir -p ${HOME}/outputs${{ matrix.dataset }} | |
| - name: participant 01 | |
| run: | | |
| docker run -t --rm --read-only \ | |
| -v ${HOME}/data/ds114_test${{ matrix.dataset }}:/bids_dataset \ | |
| -v ${HOME}/outputs${{ matrix.dataset }}:/outputs \ | |
| -v ${HOME}/license/license.txt:/license.txt \ | |
| --tmpfs /tmp \ | |
| --tmpfs /var/tmp \ | |
| bids/freesurfer:latest \ | |
| /bids_dataset /outputs participant \ | |
| --license_file=/license.txt --stages autorecon1 | |
| cat ${HOME}/outputs${{ matrix.dataset }}/sub-01/scripts/recon-all.done | |
| - name: check output | |
| run: tree ${HOME}/outputs${{ matrix.dataset }} |