基因容器 GCS
基因容器 GCS
- 最新动态
- 产品介绍
- 快速入门
- 用户指南
- Cromwell引擎使用指南
- 最佳实践
- 流程语法参考
- Python SDK参考
- API参考
-
CLI参考
- 命令总览
- 安装命令行工具
- 示例：使用命令行执行简单脚本
-
gcs 命令详情
- gcs version
- gcs config add
- gcs config list
- gcs get kubectl
- gcs get enviroment
- gcs set env
- gcs get sfs
- gcs set sfs
- gcs get obscli
- gcs obs upload
- gcs get workflow
- gcs create workflow
- gcs del workflow
- gcs update workflow
- gcs sub workflow
- gcs get execution
- gcs create execution
- gcs del execution
- gcs set execution
- gcs sub job
- gcs sub repjob
- gcs get tool
- gcs sub wdl
- gcs get wdl
- gcs set wdl
- get get fr
- config.ini配置说明
- 常见问题
- 视频帮助
- 文档下载
- 通用参考
本文导读
链接复制成功！
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：
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 |
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
