Toil K8S experiment job

rna-seq-job.yaml

apiVersion: batch/v1
kind: Job
metadata:
  # It is good practice to include your username in your job name.
  # Also specify it in TOIL_KUBERNETES_OWNER
  name: tthyer-toil-rna-seq-test

spec:
  # Do not try and rerun the leader job if it fails
  backoffLimit: 0
  template:
    spec:
      restartPolicy: Never
      serviceAccountName: default
      volumes:
      - name: synapse-secret-volume
        secret:
          secretName: synapse-config
      containers:
      - name: main
        image: quay.io/tessthyer/toil:4.1.0a1-23a56ee84a4e43f9ea8e2730d5969f71b27774c9-py3.7
        imagePullPolicy: Always
        volumeMounts:
        - name: synapse-secret-volume
          readOnly: true
          mountPath: "/tmp/.synapseConfig"
          subPath: ".synapseConfig"
        env:
        # Specify your username for inclusion in job names
        - name: TOIL_KUBERNETES_OWNER
          value: tthyer
        - name: SYNAPSE_SECRET_NAME
          value: synapse-config
        resources:
          # Make sure to set these resource limits to values large enough
          # to accomodate the work your workflow does in the leader
          # process, but small enough to fit on your cluster.
          #
          # Since no request values are specified, the limits are also used
          # for the requests.
          limits:
            cpu: 2
            memory: "4Gi"
            ephemeral-storage: "10Gi"
        command:
        - /bin/bash
        - -c
        - |
          # This Bash script will set up Toil and the workflow to run, and run them.
          set -e
          
          # We make sure to create a work directory; Toil can't hot-deploy a
          # script from the root of the filesystem, which is where we start.
          mkdir /tmp/work
          cd /tmp/work
          
          # We make a virtual environment to allow workflow dependencies to be
          # hot-deployed.
          #
          # We don't really make use of it in this example, but for workflows
          # that depend on PyPI packages we will need this.
          #
          # We use --system-site-packages so that the Toil installed in the
          # appliance image is still available.
          virtualenv --python python3 --system-site-packages venv
          . venv/bin/activate
          
          # Now clone the dockstore-workflow-rnaseq git repository
          git clone https://github.com/tthyer/dockstore-workflow-rnaseq.git
          cd dockstore-workflow-rnaseq
          git checkout toil-k8s-experiment
          
          # Now we run the workflow
          #./utils/run-toil.py jobs/test-paired-bam
          mkdir -p /var/log/toil/workers/def
          toil-cwl-runner \
            --batchSystem kubernetes \
            --jobStore aws:us-east-1:tthyer-toil-k8s-test-def \
            --logLevel DEBUG \
            --logFile /var/log/toil/def.log \
            --writeLogs /var/log/toil/workers/def \
            --targetTime 1 \
            --defaultDisk 400G \
            --nodeTypes m5.4xlarge \
            --maxNodes 3 \
            --nodeStorage 400 \
            --destBucket s3://tthyer-toil-k8s-test-out \
            --rescueJobsFrequency 9000 \
            --preserve-entire-environment \
            --retryCount 0 \
            bam_paired.cwl jobs/test-paired-bam/job.json