pipeline-frameworks-cromwell-03.数据库配置

mysql 镜像获取

https://github.com/PSC-PublicHealth/mysql-singularity-container/blob/master/README.md

启动singularity 服务

一次执行如下shell

1. sh instance.sh

   #!/bin/bash
   mkdir -p ${PWD}/mysql/var/lib/mysql ${PWD}/mysql/run/mysqld
   /share/app/singularity/3.8.1/bin/singularity instance start \
       --bind ${PWD}/mysql/var/lib/mysql/:/var/lib/mysql \
       --bind ${PWD}/mysql/run/mysqld:/run/mysqld \
      ./mysql.simg mysql

2. sh mysql_server.sh 启动mysql 服务

   /share/app/singularity/3.8.1/bin/singularity run instance://mysql

3. 创建文件 cromwell.sql

   CREATE DATABASE IF NOT EXISTS cromwell default charset utf8mb4 COLLATE utf8mb4_unicode_ci;
   CREATE USER IF NOT EXISTS 'cromwell'@'localhost' IDENTIFIED BY 'cromwell';
   GRANT all privileges ON cromwell.* TO 'cromwell'@'localhost';
   grant all privileges on *.* to 'root'@'127.0.0.1' identified by 'root';
   grant all privileges on *.* to 'cromwell'@'127.0.0.1' identified by 'cromwell';
   flush privileges;

4. sh cromwell_init.sh 创建mysql中的cromwel调度相关表结构

   /share/app/singularity/3.8.1/bin/singularity exec instance://mysql mysql < cromwell.sql