更新时间:2022-05-05 GMT+08:00
单一步骤(一个并发)
命令示例
首先以执行单一命令为例。以 gcs sub job 为例,我们使用:
gcs sub job --cpu 0.5 --memory 1g --tool bwa:0.7.12 --shell sh bwa_help.sh
生成GCS流程示例
该命令将会生成以下模板,并提交基因容器语法解析器:
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version: genecontainer_0_1
inputs:
memory:
default: 1g
type: string
cpu:
default: 0.5c
type: string
tool:
default: bwa:0.7.12
type: string
job-script:
default: bwa_help.sh
type: string
jobid:
default: bwa-help-2018-0830-171114-00d34
type: string
shell:
default: sh
type: string
workflow:
bwa-help-2018-0830-171114-00d34:
tool: bwa:0.7.12
type: GCS.Job
resources:
memory: ${memory}
cpu: ${cpu}
commands:
- sh /obs/gcscli/bwa-help-2018-0830-171114-00d34/bwa_help.sh
volumes:
sample-data:
mount_path: /obs
mount_from:
pvc: ${GCS_DATA_PVC}
temp-data:
mount_path: /sfs
mount_from:
pvc: ${GCS_SFS_PVC}
ref-data:
mount_path: /ref
mount_from:
pvc: ${GCS_REF_PVC}
outputs:
bwa-help-2018-0830-171114-00d34:
path:
- /obs/output/bwa-help-2018-0830-171114-00d34
|
生成 Kubernetes示例
该模板将进一步解析成以下 Kubernetes 模板 ,并提交云容器引擎:
kind: Job apiVersion: batch/v1 metadata: name: bwa-help-2018-0830-171114-00d34-0-81419ff7ad0d11e8 namespace: default selfLink: >- /apis/batch/v1/namespaces/default/jobs/bwa-help-2018-0830-171114-00d34-0-81419ff7ad0d11e8 uid: 815b643b-ad0d-11e8-aba9-fa163ed435e0 resourceVersion: '706141' labels: gcs.execution.id: 81419ff7-ad0d-11e8-bebc-0255ac1066a1 gcs.execution.name: gcs-2018-0830-171114-1-0-2018-0830-171114-35d77 gcs.source.name: bwa-help-2018-0830-171114-00d34 source: gcs stack-name: gcs-2018-0830-171114-1-0-2018-0830-171114-35d77 spec: parallelism: 1 completions: 1 backoffLimit: 6 selector: matchLabels: controller-uid: 815b643b-ad0d-11e8-aba9-fa163ed435e0 template: metadata: creationTimestamp: null labels: controller-uid: 815b643b-ad0d-11e8-aba9-fa163ed435e0 gcs.execution.id: 81419ff7-ad0d-11e8-bebc-0255ac1066a1 gcs.execution.name: gcs-2018-0830-171114-1-0-2018-0830-171114-35d77 gcs.source.name: bwa-help-2018-0830-171114-00d34 job-name: bwa-help-2018-0830-171114-00d34-0-81419ff7ad0d11e8 source: gcs spec: volumes: - name: sample-data persistentVolumeClaim: claimName: XXXXXXXXX - name: temp-data persistentVolumeClaim: claimName: XXXXXXXXX - name: ref-data persistentVolumeClaim: claimName: XXXXXXXXX containers: - name: bwa-help-2018-0830-171114-00d34-0-81419ff7ad0d11e8 image: '100.125.5.235:20202/genecontainer/bwa:0.7.12-r1039-sam18-sbb67' command: - sh - '-c' - sh /obs/gcscli/bwa-help-2018-0830-171114-00d34/bwa_help.sh resources: requests: cpu: '0.5' memory: 1G volumeMounts: - name: sample-data mountPath: /obs - name: temp-data mountPath: /sfs - name: ref-data mountPath: /ref terminationMessagePath: /dev/termination-log terminationMessagePolicy: File imagePullPolicy: IfNotPresent restartPolicy: OnFailure terminationGracePeriodSeconds: 30 dnsPolicy: ClusterFirst securityContext: {} affinity: podAffinity: preferredDuringSchedulingIgnoredDuringExecution: - weight: 1 podAffinityTerm: labelSelector: matchLabels: source: gcs topologyKey: kubernetes.io/hostname schedulerName: default-scheduler
父主题: 流程语法示例