April 2022
Beginner to intermediate
486 pages
10h 22m
Chinese
Content preview from 云端基因组学
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289
第
10
章
用
Pipelines API
运行
多个工作流
第
8
章我们首次运行工作流，当时用的是我们在
GCP
平台自定义的一台虚拟机。然
而单台机器的配置无法让我们利用云的最大优势：云端按需提供似乎无穷无尽的机
器！因此本章我们用
GCP
平台提供的基因组流水线接口（
Genomics Pipelines API
，
PAPI
）服务来运行工作流。
PAPI
是
GCP
平台计算引擎实例的一种作业调度服务。
首先我们修改虚拟机
Cromwell
系统的配置，使其将作业交给
PAPI
而非本地机器处
理。接着我们用
WDL_Runner
工具，封装
Cromwell
并管理提交给
PAPI
的作业，使
其易于“启动和忘记”
WDL
的执行。本章前半部分所探讨的两种方法，将为我们敞
开全规模运行
GATK
流水线的大门，而这是无法用第
9
章单台虚拟机配置来完成的。
期间我们还将讨论运行时间、成本、可移植性和整体效率等在云端运行工作流所要
考虑的重要事项。
10.1 GCP
平台
PAPI
服务简介
PAPI
是
GCP
平台经营的一项服务，它降低用户发送作业、交
GCP
平台计算引擎执
行的难度，使其无需直接管理虚拟机。尽管它的英文全名叫作“
Genomics Pipelines
API
”，但
PAPI
实际并非专用于基因组分析，它还可以用在许多其他的工作和应
用场景。我们通常简称其为
Pipelines API
或
PAPI
。直接按照谷歌云文档（
https://
290
｜
第
10
章
oreil.ly/l3OBw
）的说明，用
PAPI
直接执行特定分析命令也是可行的，但本章目标
是在用
Cromwell ...
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I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.Addison B.
I’ve been on the O’Reilly platform for more than eight years. I use a couple of learning platforms, but I'm on O'Reilly more than anybody else. When you're there, you start learning. I'm never disappointed.Amir M.
I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.