April 2022
Beginner to intermediate
486 pages
10h 22m
Chinese
Content preview from 云端基因组学
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260
｜
第
8
章
$ java -jar $BIN/cromwell-48.jar \
run $WF/scatter-hc/scatter-haplotypecaller.wdl \
-i $WF/scatter-hc/scatter-haplotypecaller.local.inputs.json
你运行该命令时，也许会注意到
Cromwell
分发的作业在你的虚拟机上并行执行。
这很棒，因为作业将快速完成。然而为处理一个完整基因组，尝试发
500
个作业，
会发生什么呢？这么多作业并行执行会引发问题；即使它们不会立即挂掉，当它们
疯狂把
RAM
中的内容写到硬盘，也会导致虚拟机宕机。好在这个问题有几种解决
方法。方法一，你可以控制
Cromwell
“本地”后端所允许的并行级别，详见在线文
档（
https://oreil.ly/8F4hp
）。方法二，使用一种专门处理这种情况的后端。第
10
章，
我们将展示如何用谷歌后端（
Google backend
）自动发送并行作业到多台虚拟机执行。
8.5.2
生成图表，实现可视化
作为该练习的结尾，让我们再多学
Womtool
工具的一种功能：
graph
命令。目前为
止，我们所探讨的工作流步骤少，整个流程非常简单。下章（以及在真实工作中），
你将遇到更复杂的工作流，对于这些工作流，你也许难以仅根据代码建立心智模式。
因此工作流如能实现可视化，对我们将非常有帮助。你可以用
Womtool
的
graph
命
令生成
.dot
格式图表文件，并用通用图表可视化工具绘制工作流：
$ java ...
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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.