nextflow源码修改及部署

[zhanglu]

1. nextflow 详情

版本： 22.10.7
本地地址：http://192.168.0.135:30080/root/nextflow.git

代码修改介绍：
K8sTaskHandler.groovy 中208行

.withHostMount(k8sConfig.get("hostPath").toString(), k8sConfig.get("hostMountPath").toString)
支持k8s模式下hostpath本地路径；

2. 部署方式：

2.1 docker

nextflow1.conf

docker {
    enabled = true
    runOptions = '-v /ceph_disk2:/ceph_disk2 --network=host --user root'
}

application.yml

server:
  port: 9081
spring:
  redis:
    host: 192.168.1.2
    port: 6379
  datasource:
    url: jdbc:postgresql://192.168.1.2:5435/qiime
    username: postgres
    password: anneng@1235_Jike2015
    driver-class-name: org.postgresql.Driver
mybatis:
  mapper-locations: classpath:mybatis/*.xml
  type-aliases-package: com.anneng.model
nextflow:
  config: /ceph_disk2/app/nextflow/genostack_nextflow_api/config/nextflow1.conf
  weblog-url: http://localhost:9081/nextflow/catchMessage
  dataPath: /ceph_disk2/app/nextflow/genostack_nextflow_api/dag
  workdir: /ceph_disk2/app/nextflow/genostack_nextflow_api/nextflow_workdir
  path: /ceph_disk2/app/nextflow/genostack_nextflow_api/nextflow-22.10.7-all
  phpsource: /ceph_disk2/data/hongyuan/data/source_v3

启动脚本：

docker run -p 9089:9081 -v /usr/bin/docker:/usr/bin/docker -v /var/run/docker.sock:/var/run/docker.sock   -v /ceph_disk2:/ceph_disk2 -v /ceph_disk2/app/nextflow/genostack_nextflow_api/config/application.yml:/application.yml -d dockerhub.genostack.com:8090/library/nextflowapi:v1.91

k8s启动方式：

nextflow1.conf

process {
   container = 'quay.io/nextflow/bash'
   executor = 'k8s'
}
k8s {
    namespace = 'default'
    hostPath = '/cephfs_data/'
    hostMountPath = '/cephfs_data/'
}

application.yml

server:
  port: 9081

spring:
  redis:
    host: 192.168.0.135
    port: 30009
  datasource:
    url: jdbc:postgresql://192.168.0.135:30008/qiime
    username: postgres
    password: anneng@1235_Jike2015
    driver-class-name: org.postgresql.Driver

mybatis:
  mapper-locations: classpath:mybatis/*.xml
  type-aliases-package: com.anneng.model

nextflow:
  config: /cephfs_data/genostack_v3/genostack_nextflow_api/config/nextflow1.conf
  weblog-url: http://localhost:9081/nextflow/catchMessage
  dataPath: /cephfs_data/genostack_v3/genostack_nextflow_api/dag
  workdir: /cephfs_data/genostack_v3/genostack_nextflow_api/nextflow_workdir
  path: nextflow
  phpsource: /cephfs_data/genostack_v3/genostack_php/source_v3

部署脚本；
sa.yaml

---
apiVersion: v1
kind: Namespace
metadata:
  name: wave-demo
---
apiVersion: v1
kind: ServiceAccount
metadata:
  namespace: wave-demo
  name: wave-sa
  annotations:
    eks.amazonaws.com/role-arn: "arn:aws:iam::011206878118:role/wave-demo-role" 
---
apiVersion: rbac.authorization.k8s.io/v1
kind: Role
metadata:
  namespace: wave-demo
  name: wave-role
rules:
  - apiGroups: [""]
    resources: ["pods", "pods/status", "pods/log", "pods/exec"]
    verbs: ["get", "list", "watch", "create", "delete"]
---
apiVersion: rbac.authorization.k8s.io/v1
kind: RoleBinding
metadata:
  namespace: wave-demo
  name: wave-rolebind
roleRef:
  apiGroup: rbac.authorization.k8s.io
  kind: Role
  name: wave-role
subjects:
  - kind: ServiceAccount
    name: wave-sa

nextflow.yaml

---
apiVersion: apps/v1
kind: Deployment
metadata:
  name: nextflow
  labels:
    app: nextflow
    layer: backend
spec:
  replicas: 1
  selector:
    matchLabels:
      app: nextflow
  template:
    metadata:
      labels:
        app: nextflow
    spec:
      serviceAccountName: wave-sa
      serviceAccount: wave-sa
      containers:             
        - name: nextflow
          image: dockerhub.genostack.com:8090/library/nextflowapi:v1.91
          ports:
            - containerPort: 9081
          volumeMounts:                                #容器内挂载点的定义部分
          - name: data                            #容器内挂载点名称
            subPath: genostack_v3/genostack_nextflow_api/config/application.yml
            mountPath: /application.yml
          - name: data
            mountPath: /cephfs_data
      volumes:                                             #本地需要挂载到容器里的数据卷定义部分
        - name: data
          hostPath:
            path: /cephfs_data
---
kind: Service
apiVersion: v1
metadata:
  name: nextflow
  labels:
    app: nextflow
    layer: backend
spec:
  type: ClusterIP
  selector:
    app: nextflow
  ports:
    - port: 9081
      targetPort: 9081

[anneng]

配置文件的优先级
Selector priority

When mixing generic process configuration and selectors the following priority rules are applied (from lower to higher):

Process generic configuration.

Process specific directive defined in the workflow script.

withLabel selector definition.

withName selector definition.